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4. Epigenetic MLH1 silencing concurs with mismatch repair deficiency in sporadic, naturally occurring colorectal cancer in rhesus macaques

Author

Deycmar, Simon, Johnson, Brendan J., Ray, Karina, Schaaf, George W., Ryan, Declan Patrick, Cullin, Cassandra, Dozier, Brandy L., Ferguson, Betsy, Bimber, Benjamin N., Olson, John D., Caudell, David L., Whitlow, Christopher T., Solingapuram Sai, Kiran Kumar, Romero, Emily C., Villinger, Francois J., Burgos, Armando G., Ainsworth, Hannah C., Miller, Lance D., Hawkins, Gregory A., Chou, Jeff W., Gomes, Bruno, Hettich, Michael, Ceppi, Maurizio, Charo, Jehad, and Cline, J. Mark

Published
2024
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6. International Consensus Statement on Obstructive Sleep Apnea

Author

Chang, Jolie L, Goldberg, Andrew N, Alt, Jeremiah A, Mohammed, Alzoubaidi, Ashbrook, Liza, Auckley, Dennis, Ayappa, Indu, Bakhtiar, Hira, Barrera, José E, Bartley, Bethany L, Billings, Martha E, Boon, Maurits S, Bosschieter, Pien, Braverman, Itzhak, Brodie, Kara, Cabrera‐Muffly, Cristina, Caesar, Ray, Cahali, Michel B, Cai, Yi, Cao, Michelle, Capasso, Robson, Caples, Sean M, Chahine, Lana M, Chang, Corissa P, Chang, Katherine W, Chaudhary, Nilika, Cheong, Crystal SJ, Chowdhuri, Susmita, Cistulli, Peter A, Claman, David, Collen, Jacob, Coughlin, Kevin C, Creamer, Jennifer, Davis, Eric M, Dupuy‐McCauley, Kara L, Durr, Megan L, Dutt, Mohan, Ali, Mazen El, Elkassabany, Nabil M, Epstein, Lawrence J, Fiala, Justin A, Freedman, Neil, Gill, Kirat, Gillespie, M Boyd, Golisch, Lea, Gooneratne, Nalaka, Gottlieb, Daniel J, Green, Katherine K, Gulati, Arushi, Gurubhagavatula, Indira, Hayward, Nathan, Hoff, Paul T, Hoffmann, Oliver MG, Holfinger, Steven J, Hsia, Jennifer, Huntley, Colin, Huoh, Kevin C, Huyett, Phillip, Inala, Sanjana, Ishman, Stacey L, Jella, Tarun K, Jobanputra, Aesha M, Johnson, Andrew P, Junna, Mithri R, Kado, Jenna T, Kaffenberger, Thomas M, Kapur, Vishesh K, Kezirian, Eric J, Khan, Meena, Kirsch, Douglas B, Kominsky, Alan, Kryger, Meir, Krystal, Andrew D, Kushida, Clete A, Kuzniar, Thomas J, Lam, Derek J, Lettieri, Christopher J, Lim, Diane C, Lin, Hsin‐Ching, Liu, Stanley YC, MacKay, Stuart G, Magalang, Ulysses J, Malhotra, Atul, Mansukhani, Meghna P, Maurer, Joachim T, May, Anna M, Mitchell, Ron B, Mokhlesi, Babak, Mullins, Anna E, Nada, Eman M, Naik, Sreelatha, Nokes, Brandon, Olson, Michael D, Pack, Allan I, Pang, Edward B, Pang, Kenny P, Patil, Susheel P, Van de Perck, Eli, Piccirillo, Jay F, and Pien, Grace W

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Health Services, Lung, Sleep Research, Clinical Research, Prevention, Respiratory, Good Health and Well Being, Adult, Humans, Sleep Apnea, Obstructive, Continuous Positive Airway Pressure, Polysomnography, Risk Factors, atrial fibrillation, cardiovascular event, cerebrovascular disease, consensus, dementia, evidence-based medicine, home sleep apnea testing, hypertension, hypoglossal nerve stimulation, mortality, motor vehicle accidents, neurocognitive function, obstructive sleep apnea, outcomes, PAP adherence, perioperative management, polysomnography, positive airway pressure, screening, sleep, sleep disordered breathing, sleepiness, sleep surgery, surgical outcomes, systematic review, treatment outcomes, uvulopalatopharyngoplasty, Immunology, Clinical sciences
Abstract

BackgroundEvaluation and interpretation of the literature on obstructive sleep apnea (OSA) allows for consolidation and determination of the key factors important for clinical management of the adult OSA patient. Toward this goal, an international collaborative of multidisciplinary experts in sleep apnea evaluation and treatment have produced the International Consensus statement on Obstructive Sleep Apnea (ICS:OSA).MethodsUsing previously defined methodology, focal topics in OSA were assigned as literature review (LR), evidence-based review (EBR), or evidence-based review with recommendations (EBR-R) formats. Each topic incorporated the available and relevant evidence which was summarized and graded on study quality. Each topic and section underwent iterative review and the ICS:OSA was created and reviewed by all authors for consensus.ResultsThe ICS:OSA addresses OSA syndrome definitions, pathophysiology, epidemiology, risk factors for disease, screening methods, diagnostic testing types, multiple treatment modalities, and effects of OSA treatment on multiple OSA-associated comorbidities. Specific focus on outcomes with positive airway pressure (PAP) and surgical treatments were evaluated.ConclusionThis review of the literature consolidates the available knowledge and identifies the limitations of the current evidence on OSA. This effort aims to create a resource for OSA evidence-based practice and identify future research needs. Knowledge gaps and research opportunities include improving the metrics of OSA disease, determining the optimal OSA screening paradigms, developing strategies for PAP adherence and longitudinal care, enhancing selection of PAP alternatives and surgery, understanding health risk outcomes, and translating evidence into individualized approaches to therapy.

Published
2023

7. A draft human pangenome reference

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K, Monlong, Jean, Abel, Haley J, Buonaiuto, Silvia, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M, Feng, Xiaowen, Fischer, Christian, Fulton, Robert S, Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T, Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J, Mitchell, Matthew W, Munson, Katherine M, Mwaniki, Moses Njagi, Novak, Adam M, Olsen, Hugh E, Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A, Sirén, Jouni, Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R, Antonacci-Fulton, Lucinda L, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Formenti, Giulio, Frankish, Adam, Gao, Yan, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Korbel, Jan O, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McCartney, Ann, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Nurk, Sergey, Olson, Nathan D, Popejoy, Alice B, Puiu, Daniela, Rautiainen, Mikko, Regier, Allison A, Rhie, Arang, Sacco, Samuel, Sanders, Ashley D, Schneider, Valerie A, Schultz, Baergen I, Shafin, Kishwar, Smith, Michael W, Sofia, Heidi J, Abou Tayoun, Ahmad N, Thibaud-Nissen, Françoise, and Tricomi, Francesca Floriana

Subjects
Biological Sciences, Genetics, 2.1 Biological and endogenous factors, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Humans, Diploidy, Genome, Human, Haplotypes, Sequence Analysis, DNA, Genomics, Reference Standards, Cohort Studies, Alleles, Genetic Variation, General Science & Technology
Abstract

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Published
2023

9. Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.

Author

Olson, Robert D, Assaf, Rida, Brettin, Thomas, Conrad, Neal, Cucinell, Clark, Davis, James J, Dempsey, Donald M, Dickerman, Allan, Dietrich, Emily M, Kenyon, Ronald W, Kuscuoglu, Mehmet, Lefkowitz, Elliot J, Lu, Jian, Machi, Dustin, Macken, Catherine, Mao, Chunhong, Niewiadomska, Anna, Nguyen, Marcus, Olsen, Gary J, Overbeek, Jamie C, Parrello, Bruce, Parrello, Victoria, Porter, Jacob S, Pusch, Gordon D, Shukla, Maulik, Singh, Indresh, Stewart, Lucy, Tan, Gene, Thomas, Chris, VanOeffelen, Margo, Vonstein, Veronika, Wallace, Zachary S, Warren, Andrew S, Wattam, Alice R, Xia, Fangfang, Yoo, Hyunseung, Zhang, Yun, Zmasek, Christian M, Scheuermann, Richard H, and Stevens, Rick L

Subjects
Influenza, Pneumonia & Influenza, Prevention, Infectious Diseases, Infection, Good Health and Well Being, Humans, Bacteria, Computational Biology, Databases, Genetic, Genomics, Influenza, Human, Viruses, Software, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.

Published
2023

10. 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

11. 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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12. Relationships Among Baseline Concussion Balance Test and Gaze Stability Test Scores in Division-I Collegiate Athletes.

Author

Quintana, Carolina P., Olson, Anne D., Heebner, Nicholas R., and Hoch, Matthew C.

Subjects
*BRAIN physiology, *SELF-evaluation, *CROSS-sectional method, *SCALE analysis (Psychology), *SPORTS injuries, *QUESTIONNAIRES, *FUNCTIONAL assessment, *DESCRIPTIVE statistics, *STATISTICAL reliability, *ATHLETIC ability, *BRAIN concussion, *POSTURAL balance, *VESTIBULAR function tests
Abstract

Context: Sports-related concussions are commonly occurring injuries as a result of sports and recreation that may cause alterations in brain functioning. It is important to be able to evaluate the impact of these injuries on function to manage the injury recovery and ensure recovery. Recent literature suggests the use of objective evaluation strategies in a multifaceted approach to evaluate and manage these injuries. It is important to understand the relationships between the assessments and how best to utilize each assessment. The purpose of this study was to investigate if relationships exist between measures of vestibular function at baseline in assessments that may be used following sports-related concussions. Additionally, a secondary purpose was to determine if self-reported symptoms were related to performance on the assessments. This study aimed to identify if these assessments measured independent functions of the vestibulo–ocular reflex or if some redundancy existed among the assessment strategies. Design: A cross-sectional study design was used in a cohort of collegiate athletes ages 18–24. Methods: Participants completed demographics questionnaires, the Post-Concussion Symptom Scale, Gaze Stabilization Test, and Concussion Balance Test. Spearman rho correlations were used to examine the relationships between the measures. Results: One hundred and thirty-five collegiate athletes (82 males and 53 females) were included, representative of 3 sports (cheerleading, soccer, and football) with a mean age of 19.77 (1.42) years old. There were weak to moderate, significant relationships between measures of Gaze Stabilization Test and Concussion Balance Test errors (r =.20–.31, P =.001–.03). Conclusions: The direction of these relationships indicated that greater Concussion Balance Test errors were associated with greater Gaze Stabilization Test performance. These relationships may be attributed to the difficulty created by the foam conditions and the integration of more complex sensory tasks required to maintain balance during the more difficult conditions. [ABSTRACT FROM AUTHOR]

Published
2024
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15. A complete reference genome improves analysis of human genetic variation

Author

Aganezov, Sergey, Yan, Stephanie M, Soto, Daniela C, Kirsche, Melanie, Zarate, Samantha, Avdeyev, Pavel, Taylor, Dylan J, Shafin, Kishwar, Shumate, Alaina, Xiao, Chunlin, Wagner, Justin, McDaniel, Jennifer, Olson, Nathan D, Sauria, Michael EG, Vollger, Mitchell R, Rhie, Arang, Meredith, Melissa, Martin, Skylar, Lee, Joyce, Koren, Sergey, Rosenfeld, Jeffrey A, Paten, Benedict, Layer, Ryan, Chin, Chen-Shan, Sedlazeck, Fritz J, Hansen, Nancy F, Miller, Danny E, Phillippy, Adam M, Miga, Karen H, McCoy, Rajiv C, Dennis, Megan Y, Zook, Justin M, and Schatz, Michael C

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Genetic Variation, Genome, Human, Genomics, Humans, Reference Standards, Sequence Analysis, DNA, General Science & Technology
Abstract

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.

Published
2022

16. 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

17. Improved MSC Minimal Criteria to Maximize Patient Safety: A Call to Embrace Tissue Factor and Hemocompatibility Assessment of MSC Products

Author

Moll, Guido, Ankrum, James A, Olson, Scott D, and Nolta, Jan A

Subjects
Medical Biotechnology, Biomedical and Clinical Sciences, Regenerative Medicine, Stem Cell Research - Nonembryonic - Human, Stem Cell Research, Stem Cell Research - Nonembryonic - Non-Human, Patient Safety, Transplantation, 5.2 Cellular and gene therapies, Development of treatments and therapeutic interventions, Generic health relevance, Blood Coagulation, Humans, Mesenchymal Stem Cell Transplantation, Mesenchymal Stem Cells, Thromboplastin, cellular therapy, mesenchymal stromal, stem cells, tissue source, product diversification, safety and efficacy, hemocompatibility, coagulation, coagulopathy, thromboembolism, tissue factor, CD142, Factor III, F3, mesenchymal stromal/stem cells, tissue factor/CD142/Factor III/F3, Biochemistry and Cell Biology, Clinical Sciences, Medical biotechnology, Biomedical engineering
Abstract

The number of mesenchymal stromal/stem cell (MSC) therapeutics and types of clinical applications have greatly diversified during the past decade, including rapid growth of poorly regulated "Stem Cell Clinics" offering diverse "Unproven Stem Cell Interventions." This product diversification necessitates a critical evaluation of the reliance on the 2006 MSC minimal criteria to not only define MSC identity but characterize MSC suitability for intravascular administration. While high-quality MSC therapeutics have been safely administered intravascularly in well-controlled clinical trials, repeated case reports of mild-to-more-severe adverse events have been reported. These are most commonly related to thromboembolic complications upon infusion of highly procoagulant tissue factor (TF/CD142)-expressing MSC products. As TF/CD142 expression varies widely depending on the source and manufacturing process of the MSC product, additional clinical cell product characterization and guidelines are needed to ensure the safe use of MSC products. To minimize risk to patients receiving MSC therapy, we here propose to supplement the minimal criteria used for characterization of MSCs, to include criteria that assess the suitability of MSC products for intravascular use. If cell products are intended for intravascular delivery, which is true for half of all clinical applications involving MSCs, the effects of MSC on coagulation and hemocompatibility should be assessed and expression of TF/CD142 should be included as a phenotypic safety marker. This adjunct criterion will ensure both the identity of the MSCs as well as the safety of the MSCs has been vetted prior to intravascular delivery of MSC products.

Published
2022

20. Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation

Author

Wallace, Zachary S, Davis, James, Niewiadomska, Anna Maria, Olson, Robert D, Shukla, Maulik, Stevens, Rick, Zhang, Yun, Zmasek, Christian M, and Scheuermann, Richard H

Subjects
Vaccine Related, Genetics, Emerging Infectious Diseases, Prevention, Pneumonia & Influenza, Biotechnology, Infectious Diseases, Immunization, Biodefense, Human Genome, Infection, Good Health and Well Being, SARS-CoV-2, bioinformatics, delta, genomic surveillance, omicron, pandemic response, variants of concern, viral evolution
Abstract

Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has demonstrated its ability to rapidly and continuously evolve, leading to the emergence of thousands of different sequence variants, many with distinctive phenotypic properties. Fortunately, the broad application of next generation sequencing (NGS) across the globe has produced a wealth of SARS-CoV-2 genome sequences, offering a comprehensive picture of how this virus is evolving so that accurate diagnostics, reliable therapeutics, and prophylactic vaccines against COVID-19 can be developed and maintained. The millions of SARS-CoV-2 sequences deposited into genomic sequencing databases, including GenBank, BV-BRC, and GISAID, are annotated with the dates and geographic locations of sample collection, and can be aligned to and compared with the Wuhan-Hu-1 reference genome to extract their constellation of nucleotide and amino acid substitutions. By aggregating these data into concise datasets, the spread of variants through space and time can be assessed. Variant tracking efforts have initially focused on the Spike protein due to its critical role in viral tropism and antibody neutralization. To identify emerging variants of concern as early as possible, we developed a computational pipeline to process the genomic data and assign risk scores based on both epidemiological and functional parameters. Epidemiological dynamics are used to identify variants exhibiting substantial growth over time and spread across geographical regions. Experimental data that quantify Spike protein regions targeted by adaptive immunity and critical for other virus characteristics are used to predict variants with consequential immunogenic and pathogenic impacts. The growth assessment and functional impact scores are combined to produce a Composite Score for any set of Spike substitutions detected. With this systematic method to routinely score and rank emerging variants, we have established an approach to identify threatening variants early and prioritize them for experimental evaluation.

Published
2022

22. Developing Impactful Summer Research Experiences for Urban Science Teachers

Author

Olson, Jennifer D., Kotche, Miiri A., Collins, Darrin, Shyjka, Andria, and Cummings, Marlon I.

Abstract

This research examines teachers' perspectives of a summer research experience for urban science teachers at an urban university with an ongoing commitment to support under-resourced schools. The program is a collaboration between the Colleges of Engineering and Education, and was developed to support urban science teachers' understanding of bioengineering concepts and effective pedagogical approaches. The program structure allows teachers to engage in bioengineering research alongside faculty and participate in workshops to support the creation of a culturally sustaining curriculum. This research seeks to highlight teachers' perspectives of the program's impact on their depth of content knowledge and pedagogical skills in an effort to contribute to the body of knowledge about developing meaningful professional development for teachers.

Published
2022
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25. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author

Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Lee, HoJoon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Olson, Nathan D., Puiu, Daniela, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sirén, Jouni, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M.D., Zimin, Aleksey V., Popejoy, Alice B., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Jarvis, Erich D., Miga, Karen H., Wang, Ting, Garrison, Erik, Marschall, Tobias, Hall, Ira, Li, Heng, Paten, Benedict, Greer, Stephanie U., Pavlichin, Dmitri S., Zhou, Bo, Urban, Alexander E., and Weissman, Tsachy

Published
2023
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26. Computational framework to capture the spatiotemporal density of cells with a cumulative environmental coupling

Author

Yereniuk, Michael A. and Olson, Sarah D.

Subjects
Mathematics - Numerical Analysis, 65M80, 35M10, 37N25
Abstract

Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel computational framework to describe and simulate stochastic cellular processes that are coupled to the environment. Specifically, through upscaling, we derive a continuum governing equation that considers the cell density as a function of time, space, and a cumulative variable that is coupled to the environmental conditions. For this new governing equation, we consider the stability through an energy analysis, as well as proving uniqueness and well-posedness. To solve the governing equations in free-space, we propose a numerical method using fundamental solutions. As an application, we study a cell moving in an infinite domain that contains a toxic chemical, where a cumulative exposure above a critical value results in cell death. We illustrate the validity of this new modeling framework and associated numerical methods by comparing the density of live cells to results from the corresponding agent-based model., Comment: 40 pages, 14 figures

Published
2019

27. A robust benchmark for detection of germline large deletions and insertions

Author

Zook, Justin M, Hansen, Nancy F, Olson, Nathan D, Chapman, Lesley, Mullikin, James C, Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M, Boutros, Paul C, Sahraeian, Sayed Mohammad E, Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E, Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T, Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L, Bashir, Ali, Jackman, Shaun, Farrell, John J, Wenger, Aaron M, Alkan, Can, Soylev, Arda, Schatz, Michael C, Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C, Rosenfeld, Jeffrey A, Zhou, Weichen, Mills, Ryan E, Sage, Jay M, Davis, Jennifer R, Kaiser, Michael D, Oliver, John S, Catalano, Anthony P, Chaisson, Mark JP, Spies, Noah, Sedlazeck, Fritz J, and Salit, Marc

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Diploidy, Genomic Structural Variation, Germ-Line Mutation, Humans, INDEL Mutation, Molecular Sequence Annotation, Sequence Analysis, DNA
Abstract

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.

Published
2020

28. Author Correction: A robust benchmark for detection of germline large deletions and insertions

Author

Zook, Justin M, Hansen, Nancy F, Olson, Nathan D, Chapman, Lesley, Mullikin, James C, Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M, Boutros, Paul C, Sahraeian, Sayed Mohammad E, Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E, Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T, Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L, Bashir, Ali, Jackman, Shaun, Farrell, John J, Wenger, Aaron M, Alkan, Can, Soylev, Arda, Schatz, Michael C, Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C, Rosenfeld, Jeffrey A, Zhou, Weichen, Mills, Ryan E, Sage, Jay M, Davis, Jennifer R, Kaiser, Michael D, Oliver, John S, Catalano, Anthony P, Chaisson, Mark JP, Spies, Noah, Sedlazeck, Fritz J, and Salit, Marc

Subjects
Control Engineering, Mechatronics and Robotics, Engineering
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

38. A hybrid cellular automaton model of cartilage regeneration capturing the interactions between cellular dynamics and scaffold porosity

Author

Cassani, Simone and Olson, Sarah D.

Subjects
Quantitative Biology - Tissues and Organs, 46N60, 62P10, 74F10, 92C117
Abstract

To accelerate the development of strategies for cartilage tissue engineering, models are necessary to study the interactions between cellular dynamics and scaffold (SC) porosity. In experiments, cells are seeded in a porous SC where over a month, the SC slowly degrades while cells divide and synthesize extracellular matrix (ECM) constituents. We use an off-lattice cellular automaton framework to model the individual behavior of cells within the SC. The movement of cells and the ability to reproduce is determined by the nutrient profile and local porosity. A phenomenological approach is used to capture a continuous profile for SC and ECM evolution, which will then change the local porosity. We parameterize the model by matching total cell counts to chondrocytes seeded in a polyglycolic acid SC. We investigate the total cell count and location of various cell populations for different initial SC porosities. Similar to experiments, we observe cell counts that level off around day 15 with higher values in SCs of lower initial porosity. Cell clustering is observed in regions at the edge of the construct that are close to the nutrient-rich medium in the fluid bath. Model results show that a bias in motion due to sensitivity to porosity allows cells to move in a more optimal arrangement. We investigate the distribution of cells as the cell reproduction rate, cell movement distance, and sensitivity to porosity is varied. We observe non monotonic changes in total cell counts within different regions of the construct due to the interplay between porosity and cellular movement. We also analyze the emergent average cell speed for different initial SC porosities, observing an higher average for the lowest initial SC porosity. This model provides a framework to further investigate how changes in biological parameters can change the cellular count and distribution in SCs of different initial porosity, Comment: 32 pages, 15 figures. Submitted to Journal of Mathematical Biology, under review

Published
2018

39. Global Density Analysis for an Off-Lattice Agent-Based Model

Author

Yereniuk, Michael A. and Olson, Sarah D.

Subjects
Mathematics - Dynamical Systems, Nonlinear Sciences - Cellular Automata and Lattice Gases
Abstract

Agent-based (AB) or Cellular Automata (CA) models are rule based and are a relatively simple discrete method that can be used to simulate complex interactions of many agents or cells. The relative ease of implementing the computational model is often counterbalanced by the difficulty of performing rigorous analysis to determine emergent behaviors. In addition, without precise definitions of cell interactions, calculating existence of fixed points and their stability is not tractable from an analytical perspective and can become computationally expensive, involving potentially thousands of simulations. Through developing a precise definition of an off-lattice CA or AB model with a specified interaction neighborhood, we develop a general method to determine a Global Recurrence Rule (GRR). This allows estimates of the state densities in time, which can be easily calculated for a range of parameters in the model. The utility of this framework is tested on an Epidemiological Cellular Automata (E-CA) model where agents or cells correspond to people that are in the susceptible, infected, or recovered states. The interaction neighborhoods of cells are determined in a mathematical formulation that allows the GRR to accurately predict the long term behavior and steady states. The modeling framework outlined will be generally applicable to many areas and can be easily extended., Comment: 32 pages, 7 figures

Published
2018

40. Emergent three-dimensional sperm motility: Coupling calcium dynamics and preferred curvature in a Kirchhoff rod model

Author

Carichino, Lucia and Olson, Sarah D.

Subjects
Mathematics - Numerical Analysis, Quantitative Biology - Cell Behavior, 92B05, 74F10, 74F25, 74K10
Abstract

Changes in calcium concentration along the sperm flagellum regulate sperm motility and hyperactivation, characterized by an increased flagellar bend amplitude and beat asymmetry, enabling the sperm to reach and penetrate the ovum (egg). The signaling pathways by which calcium increases within the flagellum are well established. However, the exact mechanisms of how calcium regulates flagellar bending are still under investigation. We extend our previous model of planar flagellar bending by developing a fluid-structure interaction model that couples the three-dimensional motion of the flagellum in a viscous, Newtonian fluid with the evolving calcium concentration. The flagellum is modeled as a Kirchhoff rod: an elastic rod with preferred curvature and twist. The calcium dynamics are represented as a one-dimensional reaction-diffusion model on a moving domain, the centerline of the flagellum. The two models are coupled assuming that the preferred curvature and twist of the sperm flagellum depend on the local calcium concentration. To investigate the effect of calcium on sperm motility, we compare model results of flagellar bend amplitude and swimming speed for three cases: planar, helical (spiral with equal amplitude in both directions), and quasi-planar (spiral with small amplitude in one direction). We observe that for the same parameters, the planar swimmer is faster and a turning motion is more clearly observed when calcium coupling is accounted for in the model. In the case of flagellar bending coupled to the calcium concentration, we observe emergent trajectories that can be characterized as a hypotrochoid for both quasi-planar and helical bending.

Published
2018
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45. Teacher Candidate Perspectives of edTPA Readiness: Preparation Programs and edTPA Supports

Author

Rao, Arthi B., Olson, Jennifer D., and Koss, Melanie D.

Abstract

This qualitative study focuses on elementary teacher candidates (TCs) at two United States university-based teacher preparation programs and their experiences with edTPA, a teacher performance assessment increasing in implementation nationwide. TCs from two public universities, in a state where edTPA bears a high-stakes connection to teaching licensure, were participants. Their perspectives of program supports that contributed to edTPA completion are emphasized. Findings suggest that particular supports within coursework and the student teaching practicum contributed to TCs' feelings of success regarding edTPA completion, while certain gaps were hindrances. Implications are applicable to teacher education programs when considering structures that may or may not be necessary for supporting TCs with edTPA.

Published
2021
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46. Examining Diverse Perspectives of edTPA Policy Implementation across States: The Good, the Bad, and the Ugly

Author

De Voto, Craig, Olson, Jennifer D., and Gottlieb, Jessica J.

Abstract

Since 2009, the Educative Teacher Performance Assessment (edTPA) has been rapidly implemented as a policy tool for strengthening teacher professionalization across the United States. However, its national assimilation has become a target for both praise and critique among teacher educators. In this article, we examine such diverse perspectives. Highlighting the sensemaking of administrators, faculty, staff, and teacher candidates (n = 75) across eight teacher preparation programs (TPPs) in two states, we examine how they have responded to varied edTPA policy designs and program contexts. Results show that both policy design and programmatic differences influence how these stakeholders have perceived and implemented edTPA--either as a framework for inquiry or compliance. In the process, we contend that edTPA has many promises and pitfalls as a scalable policy tool for preparing and assessing future teachers.

Published
2021
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48. 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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