25 results on '"Alexandra P. Lewis"'
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2. Beneficial impacts of neuromuscular electrical stimulation on muscle structure and function in the zebrafish model of Duchenne muscular dystrophy
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Elisabeth A Kilroy, Amanda C Ignacz, Kaylee L Brann, Claire E Schaffer, Devon Varney, Sarah S Alrowaished, Kodey J Silknitter, Jordan N Miner, Ahmed Almaghasilah, Tashawna L Spellen, Alexandra D Lewis, Karissa Tilbury, Benjamin L King, Joshua B Kelley, and Clarissa A Henry
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neuromuscular development ,dystroglycanopathies ,skeletal muscle ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Neuromuscular electrical stimulation (NMES) allows activation of muscle fibers in the absence of voluntary force generation. NMES could have the potential to promote muscle homeostasis in the context of muscle disease, but the impacts of NMES on diseased muscle are not well understood. We used the zebrafish Duchenne muscular dystrophy (dmd) mutant and a longitudinal design to elucidate the consequences of NMES on muscle health. We designed four neuromuscular stimulation paradigms loosely based on weightlifting regimens. Each paradigm differentially affected neuromuscular structure, function, and survival. Only endurance neuromuscular stimulation (eNMES) improved all outcome measures. We found that eNMES improves muscle and neuromuscular junction morphology, swimming, and survival. Heme oxygenase and integrin alpha7 are required for eNMES-mediated improvement. Our data indicate that neuromuscular stimulation can be beneficial, suggesting that the right type of activity may benefit patients with muscle disease.
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- 2022
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3. A draft human pangenome reference
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Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Charles Markello, Fergal J. Martin, Matthew W. Mitchell, Katherine M. Munson, Moses Njagi Mwaniki, Adam M. Novak, Hugh E. Olsen, Trevor Pesout, David Porubsky, Pjotr Prins, Jonas A. Sibbesen, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Lucinda L. Antonacci-Fulton, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Andrew Carroll, Pi-Chuan Chang, Sarah Cody, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Peter Ebert, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Giulio Formenti, Adam Frankish, Yan Gao, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Leanne Haggerty, Kendra Hoekzema, Thibaut Hourlier, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Ann McCartney, Jennifer McDaniel, Jacquelyn Mountcastle, Maria Nattestad, Sergey Nurk, Nathan D. Olson, Alice B. Popejoy, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Francesca Floriana Tricomi, Justin Wagner, Brian Walenz, Jonathan M. D. Wood, Aleksey V. Zimin, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin M. Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H. Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li, and Benedict Paten
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Cancer Research ,Multidisciplinary - 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.
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- 2023
4. Recombination between heterologous human acrocentric chromosomes
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Barcelona Supercomputing Center, Human Pangenome Reference Consortium: "Haley J. Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark J. P. Chaisson, Pi-Chuan Chang, Xian H. Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Jana Ebler, Evan E. Eichler, Jordan M. Eizenga, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Yan Gao, Shilpa Garg, Erik Garrison, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Glenn Hickey, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Heng Li, Wen-Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian K. Lucas, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann McCartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jean Monlong, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Adam M. Novak, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Benedict Paten, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubsky, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Jonas A. Sibbesen, Jouni Sirén, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Chad Tomlinson, Francesca Floriana Tricomi, Flavia Villani, Mitchell R. Vollger, Justin Wagner, Brian Walenz, Ting Wang, Jonathan M. D. Wood, Aleksey, Guarracino, Andrea, Buonaiuto, Silvia, Gomes de Lima, Leonardo, Potapova, Tamara, Rhie, Arang, Marco, Santiago, Barcelona Supercomputing Center, Human Pangenome Reference Consortium: "Haley J. Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark J. P. Chaisson, Pi-Chuan Chang, Xian H. Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Jana Ebler, Evan E. Eichler, Jordan M. Eizenga, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Yan Gao, Shilpa Garg, Erik Garrison, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Glenn Hickey, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Heng Li, Wen-Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian K. Lucas, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann McCartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jean Monlong, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Adam M. Novak, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Benedict Paten, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubsky, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Jonas A. Sibbesen, Jouni Sirén, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Chad Tomlinson, Francesca Floriana Tricomi, Flavia Villani, Mitchell R. Vollger, Justin Wagner, Brian Walenz, Ting Wang, Jonathan M. D. Wood, Aleksey, Guarracino, Andrea, Buonaiuto, Silvia, Gomes de Lima, Leonardo, Potapova, Tamara, Rhie, Arang, and Marco, Santiago
- Abstract
The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications1,2. Although the resolution of these regions in the first complete assembly of a human genome—the Telomere-to-Telomere Consortium’s CHM13 assembly (T2T-CHM13)—provided a model of their homology3, it remained unclear whether these patterns were ancestral or maintained by ongoing recombination exchange. Here we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologous sequences. Utilizing an all-to-all comparison of the human pangenome from the Human Pangenome Reference Consortium4 (HPRC), we find that contigs from all of the SAACs form a community. A variation graph5 constructed from centromere-spanning acrocentric contigs indicates the presence of regions in which most contigs appear nearly identical between heterologous acrocentric chromosomes in T2T-CHM13. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the pseudo-homologous regions than in the corresponding short and long arms, indicating higher rates of recombination6,7. The pseudo-homologous regions include sequences that have previously been shown to lie at the breakpoint of Robertsonian translocations8, and their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14 and 21. The ubiquity of signals of recombination between heterologous acrocentric chromosomes seen in the HPRC draft pangenome suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed from cytogenetic studies 50 years ago9., Our work depends on the HPRC draft human pangenome resource established in the accompanying Article4, and we thank the production and assembly groups for their efforts in establishing this resource. This work used the computational resources of the UTHSC Octopus cluster and NIH HPC Biowulf cluster. We acknowledge support in maintaining these systems that was critical to our analyses. The authors thank M. Miller for the development of a graphical synopsis of our study (Fig. 5); and R. Williams and N. Soranzo for support and guidance in the design and discussion of our work. This work was supported, in part, by National Institutes of Health/NIDA U01DA047638 (E.G.), National Institutes of Health/NIGMS R01GM123489 (E.G.), NSF PPoSS Award no. 2118709 (E.G. and C.F.), the Tennessee Governor’s Chairs programme (C.F. and E.G.), National Institutes of Health/NCI R01CA266339 (T.P., L.G.d.L. and J.L.G.), and the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (A.R., S.K. and A.M.P.). We acknowledge support from Human Technopole (A.G.), Consiglio Nazionale delle Ricerche, Italy (S.B. and V.C.), and Stowers Institute for Medical Research (T.P., L.G.d.L., B.R. and J.L.G.)., Peer Reviewed, "Article signat per 13 autors/es: Andrea Guarracino, Silvia Buonaiuto, Leonardo Gomes de Lima, Tamara Potapova, Arang Rhie, Sergey Koren, Boris Rubinstein, Christian Fischer, Human Pangenome Reference Consortium, Jennifer L. Gerton, Adam M. Phillippy, Vincenza Colonna & Erik Garrison " Human Pangenome Reference Consortium: "Haley J. Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark J. P. Chaisson, Pi-Chuan Chang, Xian H. Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Jana Ebler, Evan E. Eichler, Jordan M. Eizenga, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Yan Gao, Shilpa Garg, Erik Garrison, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Glenn Hickey, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Heng Li, Wen-Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian K. Lucas, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann McCartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jean Monlong, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Adam M. Novak, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Benedict Paten, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubsky, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. S, Postprint (published version)
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- 2023
5. Structurally divergent and recurrently mutated regions of primate genomes
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Yafei Mao, William T. Harvey, David Porubsky, Katherine M. Munson, Kendra Hoekzema, Alexandra P. Lewis, Peter A. Audano, Allison Rozanski, Xiangyu Yang, Shilong Zhang, David S. Gordon, Xiaoxi Wei, Glennis A. Logsdon, Marina Haukness, Philip C. Dishuck, Hyeonsoo Jeong, Ricardo del Rosario, Vanessa L. Bauer, Will T. Fattor, Gregory K. Wilkerson, Qing Lu, Benedict Paten, Guoping Feng, Sara L. Sawyer, Wesley C. Warren, Lucia Carbone, and Evan E. Eichler
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Article - Abstract
To better understand the pattern of primate genome structural variation, we sequenced and assembled using multiple long-read sequencing technologies the genomes of eight nonhuman primate species, including New World monkeys (owl monkey and marmoset), Old World monkey (macaque), Asian apes (orangutan and gibbon), and African ape lineages (gorilla, bonobo, and chimpanzee). Compared to the human genome, we identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. Across 50 million years of primate evolution, we estimate that 819.47 Mbp or ~27% of the genome has been affected by SVs based on analysis of these primate lineages. We identify 1,607 structurally divergent regions (SDRs) wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (CARDs,ABCD7,OLAH) and new lineage-specific genes are generated (e.g.,CKAP2,NEK5) and have become targets of rapid chromosomal diversification and positive selection (e.g.,RGPDs). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species for the first time.
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- 2023
6. Familial long-read sequencing increases yield of de novo mutations
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Michelle D. Noyes, William T. Harvey, David Porubsky, Arvis Sulovari, Ruiyang Li, Nicholas R. Rose, Peter A. Audano, Katherine M. Munson, Alexandra P. Lewis, Kendra Hoekzema, Tuomo Mantere, Tina A. Graves-Lindsay, Ashley D. Sanders, Sara Goodwin, Melissa Kramer, Younes Mokrab, Michael C. Zody, Alexander Hoischen, Jan O. Korbel, W. Richard McCombie, and Evan E. Eichler
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All institutes and research themes of the Radboud University Medical Center ,Nucleotides ,Mutation ,lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4] ,Genetics ,High-Throughput Nucleotide Sequencing ,Humans ,Female ,Genomics ,Sequence Analysis, DNA ,Software ,Article ,Genetics (clinical) - Abstract
Studies of de novo mutation (DNM) have typically excluded some of the most repetitive and complex regions of the genome because these regions cannot be unambiguously mapped with short-read sequencing data. To better understand the genome-wide pattern of DNM, we generated long-read sequence data from an autism parent-child quad with an affected female where no pathogenic variant had been discovered in short-read Illumina sequence data. We deeply sequenced all four individuals by using three sequencing platforms (Illumina, Oxford Nanopore, and Pacific Biosciences) and three complementary technologies (Strand-seq, optical mapping, and 10X Genomics). Using long-read sequencing, we initially discovered and validated 171 DNMs across two children—a 20% increase in the number of de novo single-nucleotide variants (SNVs) and indels when compared to short-read callsets. The number of DNMs further increased by 5% when considering a more complete human reference (T2T-CHM13) because of the recovery of events in regions absent from GRCh38 (e.g., three DNMs in heterochromatic satellites). In total, we validated 195 de novo germline mutations and 23 potential post-zygotic mosaic mutations across both children; the overall true substitution rate based on this integrated callset is at least 1.41 × 10(−8) substitutions per nucleotide per generation. We also identified six de novo insertions and deletions in tandem repeats, two of which represent structural variants. We demonstrate that long-read sequencing and assembly, especially when combined with a more complete reference genome, increases the number of DNMs by >25% compared to previous studies, providing a more complete catalog of DNM compared to short-read data alone.
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- 2022
7. The complete sequence of a human Y chromosome
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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.
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- 2022
8. A high-quality bonobo genome refines the analysis of hominid evolution
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Melanie Sorensen, Yafei Mao, Sofie R. Salama, Claudia Rita Catacchio, Andy Wing Chun Pang, Françoise Thibaud-Nissen, Carl Baker, LaDeana W. Hillier, Ruiyang Li, Arvis Sulovari, Philip C. Dishuck, PingHsun Hsieh, Katherine M. Munson, Ludovica Mercuri, Jason D Fernandes, Jessica M. Storer, Joyce V. Lee, Benedict Paten, Mark A. Batzer, Peter A. Audano, David Porubsky, Tzu-Hsueh Huang, Jason G. Underwood, Evan E. Eichler, Jinna Hoffman, William T. Harvey, Kendra Hoekzema, Jerilyn A. Walker, Ian T. Fiddes, David Gordon, Marina Haukness, Alex Hastie, Alexandra P. Lewis, Francesca Antonacci, Mario Ventura, Shwetha C. Murali, Francesco Montinaro, Ilaria Piccolo, and Mark Diekhans
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Pan troglodytes ,Sequence assembly ,Genomics ,Biology ,Genome informatics ,Genome ,Article ,Evolutionary genetics ,Coalescent theory ,Evolution, Molecular ,03 medical and health sciences ,Segmental Duplications, Genomic ,0302 clinical medicine ,Animals ,Sequencing ,Phylogeny ,030304 developmental biology ,Segmental duplication ,0303 health sciences ,Gorilla gorilla ,Multidisciplinary ,Bonobo ,Pongo ,Molecular Sequence Annotation ,Sequence Analysis, DNA ,Pan paniscus ,biology.organism_classification ,Genome evolution ,Genes ,Evolutionary biology ,Eukaryotic Initiation Factor-4A ,Female ,Human genome ,Mobile genetic elements ,030217 neurology & neurosurgery - Abstract
The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes1,3–5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome., A high-quality bonobo genome assembly provides insights into incomplete lineage sorting in hominids and its relevance to gene evolution and the genetic relationship among living hominids.
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- 2021
9. Segmental duplications and their variation in a complete human genome
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Mitchell R. Vollger, Xavi Guitart, Philip C. Dishuck, Ludovica Mercuri, William T. Harvey, Ariel Gershman, Mark Diekhans, Arvis Sulovari, Katherine M. Munson, Alexandra P. Lewis, Kendra Hoekzema, David Porubsky, Ruiyang Li, Sergey Nurk, Sergey Koren, Karen H. Miga, Adam M. Phillippy, Winston Timp, Mario Ventura, and Evan E. Eichler
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Multidisciplinary ,Article - Abstract
Despite their importance in disease and evolution, highly identical segmental duplications (SDs) are among the last regions of the human reference genome (GRCh38) to be fully sequenced. Using a complete telomere-to-telomere human genome (T2T-CHM13), we present a comprehensive view of human SD organization. SDs account for nearly one-third of the additional sequence, increasing the genome-wide estimate from 5.4 to 7.0% [218 million base pairs (Mbp)]. An analysis of 268 human genomes shows that 91% of the previously unresolved T2T-CHM13 SD sequence (68.3 Mbp) better represents human copy number variation. Comparing long-read assemblies from human ( n = 12) and nonhuman primate ( n = 5) genomes, we systematically reconstruct the evolution and structural haplotype diversity of biomedically relevant and duplicated genes. This analysis reveals patterns of structural heterozygosity and evolutionary differences in SD organization between humans and other primates.
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- 2022
10. Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans
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Mitchell R. Vollger, Katherine M. Munson, Philip C. Dishuck, Vy Dang, Yafei Mao, PingHsun Hsieh, Tzu-Hsueh Huang, Melanie Sorensen, Alexandra P. Lewis, Carl Baker, AnneMarie E. Welch, Stuart Cantsilieris, Jason G. Underwood, and Evan E. Eichler
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DNA Copy Number Variations ,Science ,General Physics and Astronomy ,Locus (genetics) ,Evolutionary biology ,Biology ,Genome informatics ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Haplogroup ,Article ,Evolution, Molecular ,Gene Duplication ,Gene duplication ,Animals ,Humans ,Copy-number variation ,Selection, Genetic ,Phylogeny ,Segmental duplication ,Neanderthals ,Multidisciplinary ,Genome, Human ,Haplotype ,Membrane Proteins ,Hominidae ,General Chemistry ,Haplotypes ,Homo sapiens - Abstract
TRP channel-associated factor 1/2 (TCAF1/TCAF2) proteins antagonistically regulate the cold-sensor protein TRPM8 in multiple human tissues. Understanding their significance has been complicated given the locus spans a gap-ridden region with complex segmental duplications in GRCh38. Using long-read sequencing, we sequence-resolve the locus, annotate full-length TCAF models in primate genomes, and show substantial human-specific TCAF copy number variation. We identify two human super haplogroups, H4 and H5, and establish that TCAF duplications originated ~1.7 million years ago but diversified only in Homo sapiens by recurrent structural mutations. Conversely, in all archaic-hominin samples the fixation for a specific H4 haplotype without duplication is likely due to positive selection. Here, our results of TCAF copy number expansion, selection signals in hominins, and differential TCAF2 expression between haplogroups and high TCAF2 and TRPM8 expression in liver and prostate in modern-day humans imply TCAF diversification among hominins potentially in response to cold or dietary adaptations., Duplications of gene segments can allow novel physiological adaptations to evolve. A detailed analysis of the TCAF gene family in primates and archaic humans suggest rapid duplication and diversification in this gene family is associated with cold or dietary adaptations.
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- 2021
11. Targeted long-read sequencing identifies missing disease-causing variation
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Tim Cherry, Seth J. Perlman, Rando Allikmets, Christina Lam, Katrina M Dipple, Alexias Safi, Hailey Loucks, Penny M Chow, Ian A. Glass, Xue Zou, Heather C Mefford, Angela Sun, Deborah A. Nickerson, Danny E. Miller, Dawn L. Earl, James T. Bennett, Alexandra P. Lewis, Stephanie Austin, Margaret P Adam, Apoorva K Iyengar, Arvis Sulovari, Edith P Almanza Fuerte, Andrew S. Allen, Audrey Squire, Karynne E. Patterson, Erin Huggins, Winston Lee, William H. Majoros, Emily S Bonkowski, Tianyun Wang, Priya S. Kishnani, Robin L. Bennett, Mary Claire King, Tara L. Wenger, Erika Beckman, Kendra Hoekzema, Gregory E. Crawford, Timothy E. Reddy, Evan E. Eichler, Irene Chang, Anne V. Hing, Zoe Nelson, Thomas J. Walsh, Dan Doherty, Megan C. Sikes, Michael J. Bamshad, Catherine R Paschal, Jessica X. Chong, Jenny Thies, and Katherine M. Munson
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Male ,DNA Copy Number Variations ,Computational biology ,Disease ,Biology ,Article ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Genetics ,Humans ,Genetic Predisposition to Disease ,Genetic Testing ,Gene ,Genetics (clinical) ,030304 developmental biology ,Sequence (medicine) ,Data source ,Chromosome Aberrations ,0303 health sciences ,Genome, Human ,Genetic Diseases, Inborn ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Phenotype ,Karyotyping ,Mutation (genetic algorithm) ,Cytogenetic Analysis ,Mutation ,Mendelian inheritance ,symbols ,Female ,Nanopore sequencing ,030217 neurology & neurosurgery - Abstract
Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.
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- 2021
12. Sequence diversity analyses of an improved rhesus macaque genome enhances its biomedical utility
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David H. O’Connor, Flavia Angela Maria Maggiolini, Claudia Rita Catacchio, Louis J. Picker, Nicholas Maurer, Jason G. Underwood, Jeffrey Rogers, Mitchell R. Vollger, Mark A. Batzer, Jeffrey A. Roberts, Ashley D. Sanders, Katherine M. Munson, Jessica M. Storer, Merly Escalona, Jon E. Levine, Muthuswamy Raveendran, Mario Ventura, Jason D Fernandes, Jan O. Korbel, Joseph W. Kemnitz, R. Alan Harris, Evan E. Eichler, Douglas L. Rosene, Shwetha C. Murali, Mark Diekhans, David Gordon, David Porubsky, Philip C. Dishuck, Erin L. Kinnally, LaDeana W. Hillier, Betsy Ferguson, Joel Armstrong, Chad Tomlinson, Zsofia Kovacs-Balint, Sara M Thomasy, Tina A. Graves-Lindsay, Roger W. Wiseman, Michael L. Platt, Peter A. Audano, Jerilyn A. Walker, Ian T. Fiddes, Benedict Paten, Elizabeth Devogelaere, David H. Abbott, J. H. Pate Skene, Marina Haukness, Mar M. Sanchez, Ned H. Kalin, Milinn Kremitzki, Alexandra P. Lewis, Francesca Antonacci, H. Michael Kubisch, Richard E. Green, John P. Capitanio, Yafei Mao, Sofie R. Salama, Ludovica Mercuri, Wesley C. Warren, Shelley A. Cole, and Stanton B. Gray
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Whole genome sequencing ,Multidisciplinary ,Genome ,Contig ,Whole Genome Sequencing ,Genetic Variation ,Molecular Sequence Annotation ,Computational biology ,Biology ,biology.organism_classification ,Macaca mulatta ,Polymorphism, Single Nucleotide ,Article ,Rhesus macaque ,Gene family ,Animals ,Humans ,Genetic Predisposition to Disease ,Indel ,Reference genome ,Segmental duplication - Abstract
A high-quality rhesus macaque genome Genome technology has improved substantially since the first full organismal genomes were generated. Applying new technology, Warren et al. refined the genome of the rhesus macaque, a model nonhuman primate. Long-read technology and other recent advances in sequencing technology were applied to generate a genome with far fewer gaps and helped to refine the locations and numbers of repetitive elements. Furthermore, the authors performed resequencing among populations to identify the genetic variability of the rhesus macaque. Thus, a previously incomplete and inaccurate set of sequence information is now fully resolved, improving gene mapping for biomedical and comparative genetic studies. Science , this issue p. eabc6617
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- 2020
13. De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation
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Zepeng Mu, Jana Ebler, PingHsun Hsieh, Kai Ye, Marta Byrska-Bishop, William T. Harvey, Mark Gerstein, Chong Li, Bernardo Rodriguez-Martin, Tobias Rausch, Michael E. Talkowski, Rebecca Serra Mari, Allison Regier, Xinghua Shi, Arvis Sulovari, Weichen Zhou, Martin Santamarina, Hufsah Ashraf, Oliver Stegle, Scott E. Devine, Yu Chen, Xuefang Zhao, Jiadong Lin, Susan Fairley, Mark Chaisson, Wolfram Höps, Alexandra P. Lewis, Ira M. Hall, Benjamin Raeder, Feyza Yilmaz, Wayne E. Clarke, Aaron M. Wenger, Qihui Zhu, Xiaofei Yang, Ashley D. Sanders, Marc Jan Bonder, Junjie Chen, Maryam Ghareghani, Katherine M. Munson, Luke J. Tallon, Evan E. Eichler, Alex Hastie, Paul Flicek, Jose M. C. Tubio, Jan O. Korbel, Peter A. Audano, Jingwen Ren, Peter Ebert, Tobias Marschall, Nelson T. Chuang, David Porubsky, Anna O. Basile, Joyce V. Lee, Yang I. Li, Harrison Brand, André Corvelo, Michael C. Zody, Patrick Hasenfeld, Ryan E. Mills, Charles Lee, Zechen Chong, Haley J. Abel, and Sushant Kumar
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Structural variation ,education.field_of_study ,Contig ,Population ,Haplotype ,Expression quantitative trait loci ,Sequence assembly ,Human genome ,Computational biology ,Biology ,education ,Genotyping - Abstract
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent–child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average contig N50: 26 Mbp) integrate all forms of genetic variation across even complex loci such as the major histocompatibility complex. We focus on 107,590 structural variants (SVs), of which 68% are inaccessible by short-read sequencing. We identify new SV hotspots (spanning megabases of gene-rich sequence), characterize 130 of the most active mobile element source elements, and find that 63% of all SVs arise by homology-mediated mechanisms—a twofold increase from previous studies. Our resource now enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1,525 expression quantitative trait loci (SV-eQTLs) as well as SV candidates for adaptive selection within the human population.
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- 2020
14. Haplotype-resolved diverse human genomes and integrated analysis of structural variation
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Tsung Yu Lu, Rebecca Serra Mari, Joyce V. Lee, Peter A. Audano, Susan Fairley, Mark Chaisson, Scott E. Devine, Ira M. Hall, Maryam Ghareghani, Sushant Kumar, Aaron M. Wenger, Jan O. Korbel, Hufsah Ashraf, Feyza Yilmaz, Tobias Marschall, Jana Ebler, Zechen Chong, Wolfram Höps, Paul Flicek, Kai Ye, Haley J. Abel, Katherine M. Munson, Jiadong Lin, Qihui Zhu, Weichen Zhou, Xiaofei Yang, Wayne E. Clarke, Michael C. Zody, Uday S. Evani, Xinghua Shi, Patrick Hasenfeld, Martin Santamarina, Bernardo Rodriguez-Martin, Tobias Rausch, Michael E. Talkowski, Jose M. C. Tubio, Luke J. Tallon, Yang I. Li, Yu Chen, Junjie Chen, André Corvelo, Zepeng Mu, PingHsun Hsieh, David Porubsky, Nelson T. Chuang, William T. Harvey, Alexandra P. Lewis, Marc Jan Bonder, Oliver Stegle, Benjamin Raeder, Xuefang Zhao, Alex Hastie, Harrison Brand, Allison A. Regier, Peter Ebert, Ryan E. Mills, Anna O. Basile, Marta Byrska-Bishop, Mark Gerstein, Chong Li, Arvis Sulovari, Jingwen Ren, Ashley D. Sanders, Charles Lee, and Evan E. Eichler
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Male ,Genotype ,Retroelements ,Population ,Quantitative Trait Loci ,Sequence assembly ,Computational biology ,Biology ,Genome ,Article ,Structural variation ,03 medical and health sciences ,0302 clinical medicine ,INDEL Mutation ,Population Groups ,Humans ,education ,030304 developmental biology ,Whole genome sequencing ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,Contig ,Whole Genome Sequencing ,Genome, Human ,Sequence Inversion ,Genetic Variation ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Interspersed Repetitive Sequences ,Haplotypes ,Expression quantitative trait loci ,Human genome ,Female ,030217 neurology & neurosurgery - Abstract
Resolving genomic structural variationMany human genomes have been reported using short-read technology, but it is difficult to resolve structural variants (SVs) using these data. These genomes thus lack comprehensive comparisons among individuals and populations. Ebertet al.used long-read structural variation calling across 64 human genomes representing diverse populations and developed new methods for variant discovery. This approach allowed the authors to increase the number of confirmed SVs and to describe the patterns of variation across populations. From this dataset, they identified quantitative trait loci affected by these SVs and determined how they may affect gene expression and potentially explain genome-wide association study hits. This information provides insights into patterns of normal human genetic variation and generates reference genomes that better represent the diversity of our species.Science, this issue p.eabf7117
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- 2020
15. Targeted long-read sequencing resolves complex structural variants and identifies missing disease-causing variants
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Ting Wang, Karynne E. Patterson, Penny M Chow, Alexandra P. Lewis, Bonkowski Es, Adam Mp, Katherine M. Munson, Catherine R Paschal, Deborah A. Nickerson, Won Hee Lee, Audrey Squire, Dipple Km, Fuerte Epa, Angela Sun, Dan Doherty, Loucks H, Christina Lam, Ian A. Glass, Danny E. Miller, Dawn L. Earl, Rando Allikmets, Jenny Thies, Chang I, Beckman E, Arvis Sulovari, Evan E. Eichler, Jessica X. Chong, Perlman Sj, Nelson Z, Kendra Hoekzema, Robin L. Bennett, Anne V. Hing, Timothy J. Cherry, Megan C. Sikes, Michael J. Bamshad, Heather C Mefford, and James T. Bennett
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Candidate gene ,symbols.namesake ,Mutation (genetic algorithm) ,Mendelian inheritance ,symbols ,Computational biology ,Nanopore sequencing ,Copy-number variation ,Biology ,Gene ,Phenotype ,Sequence (medicine) - Abstract
BACKGROUNDDespite widespread availability of clinical genetic testing, many individuals with suspected genetic conditions do not have a precise diagnosis. This limits their opportunity to take advantage of state-of-the-art treatments. In such instances, testing sometimes reveals difficult-to-evaluate complex structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in specific genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted.METHODSTargeted long-read sequencing (T-LRS) was performed on 33 individuals using Read Until on the Oxford Nanopore platform. This method allowed us to computationally target up to 100 Mbp of sequence per experiment, resulting in an average of 20x coverage of target regions, a 500% increase over background. We analyzed patient DNA for pathogenic substitutions, structural variants, and methylation differences using a single data source.RESULTSThe effectiveness of T-LRS was validated by detecting all genomic aberrations, including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences, previously identified by prior clinical testing. In 6/7 individuals who had complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, which led, in one case, to a change in clinical management. In nine individuals with suspected Mendelian conditions who lacked a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in five and variants of uncertain significance in two others.CONCLUSIONST-LRS can accurately predict pathogenic copy number variants and triplet repeat expansions, resolve complex rearrangements, and identify single-nucleotide variants not detected by other technologies, including short-read sequencing. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority candidate genes and regions or to further evaluate complex clinical testing results. The application of T-LRS will likely increase the diagnostic rate of rare disorders.
- Published
- 2020
16. Opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans
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Alexandra P. Lewis, PingHsun Hsieh, Jason G. Underwood, Yafei Mao, AnneMarie E. Welch, Mitchell R. Vollger, Tzu-Hsueh Huang, Vy Dang, Carl Baker, Stuart Cantsilieris, Katherine M. Munson, Philip C. Dishuck, Evan E. Eichler, and Melanie Scofield
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Evolutionary biology ,Biology ,Human specific ,Gene - Abstract
TRP channel-associated factor 1/2 (TCAF1/TCAF2) proteins antagonistically regulate the cold-sensor protein TRPM8 in multiple human tissues. Understanding their significance has been complicated given the locus spans a gap-ridden region with complex segmental duplications in GRCh38. Using long-read sequencing, we sequence-resolve the locus, annotate full-length TCAF models in human and nonhuman primate genomes, and show substantial human-specific TCAF copy number variation. We identify two human super haplogroups, H4 and H5, and establish that TCAF duplications originated ~1.7 million years ago but diversified only in Homo sapiens by recurrent structural mutations that altered TCAF copy number and regulation. Conversely, in all archaic-hominin samples the fixation for a specific H4 haplotype without duplication is likely due to positive selection. The significant, positive effect of H4 on TCAF2 expression in modern-day humans with candidate associations for hypothyroidism, nerve compression, and diabetes suggests TCAF diversification among hominins potentially in response to cold or dietary adaptations.
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- 2020
17. Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes
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Katherine M. Munson, Evan E. Eichler, PingHsun Hsieh, Flavia Angela Maria Maggiolini, Giorgia Chiatante, Alexandra P. Lewis, Francesca Antonacci, Vy Dang, Carl Baker, Stuart Cantsilieris, David Porubsky, Bradley J. Nelson, Shwetha C. Murali, Melanie Sorensen, Jean-François Deleuze, Kendra Hoekzema, Jason G. Underwood, Mitchell R. Vollger, Hélène Blanché, and Zev N. Kronenberg
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DNA Copy Number Variations ,Introgression ,Biology ,Genetic Introgression ,Genome ,Article ,Evolution, Molecular ,mental disorders ,Chromosome Duplication ,Genetic variation ,Animals ,Humans ,Copy-number variation ,Selection, Genetic ,Neanderthals ,Whole genome sequencing ,Polymorphism, Genetic ,Multidisciplinary ,Models, Genetic ,Whole Genome Sequencing ,Genome, Human ,Haplotype ,Hominidae ,Haplotypes ,Evolutionary biology ,Human genome ,Melanesia ,Adaptation ,Chromosomes, Human, Pair 16 ,Chromosomes, Human, Pair 8 - Abstract
Adaptive archaic hominin genes As they migrated out of Africa and into Europe and Asia, anatomically modern humans interbred with archaic hominins, such as Neanderthals and Denisovans. The result of this genetic introgression on the recipient populations has been of considerable interest, especially in cases of selection for specific archaic genetic variants. Hsieh et al. characterized adaptive structural variants and copy number variants that are likely targets of positive selection in Melanesians. Focusing on population-specific regions of the genome that carry duplicated genes and show an excess of amino acid replacements provides evidence for one of the mechanisms by which genetic novelty can arise and result in differentiation between human genomes. Science , this issue p. eaax2083
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- 2019
18. Recurrent somatic loss ofTNFRSF14in classical Hodgkin lymphoma
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Andrew Adey, Jay Shendure, Anju Thomas, Alexandra P. Lewis, Stephen J. Salipante, David Wu, Jonathan R. Fromm, Akash Kumar, Choli Lee, and Yajuan J. Liu
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0301 basic medicine ,Cancer Research ,education.field_of_study ,medicine.diagnostic_test ,Somatic cell ,Population ,Copy number analysis ,Cell sorting ,Biology ,medicine.disease_cause ,medicine.disease ,Molecular biology ,Flow cytometry ,03 medical and health sciences ,030104 developmental biology ,Reed–Sternberg cell ,Cell culture ,Immunology ,Genetics ,medicine ,Carcinogenesis ,education - Abstract
Investigation of the genetic lesions underlying classical Hodgkin lymphoma (CHL) has been challenging due to the rarity of Hodgkin and Reed-Sternberg (HRS) cells, the pathognomonic neoplastic cells of CHL. In an effort to catalog more comprehensively recurrent copy number alterations occurring during oncogenesis, we investigated somatic alterations involved in CHL using whole-genome sequencing-mediated copy number analysis of purified HRS cells. We performed low-coverage sequencing of small numbers of intact HRS cells and paired non-neoplastic B lymphocytes isolated by flow cytometric cell sorting from 19 primary cases, as well as two commonly used HRS-derived cell lines (KM-H2 and L1236). We found that HRS cells contain strikingly fewer copy number abnormalities than CHL cell lines. A subset of cases displayed nonintegral chromosomal copy number states, suggesting internal heterogeneity within the HRS cell population. Recurrent somatic copy number alterations involving known factors in CHL pathogenesis were identified (REL, the PD-1 pathway, and TNFAIP3). In eight cases (42%) we observed recurrent copy number loss of chr1:2,352,236-4,574,271, a region containing the candidate tumor suppressor TNFRSF14. Using flow cytometry, we demonstrated reduced TNFRSF14 expression in HRS cells from 5 of 22 additional cases (23%) and in two of three CHL cell lines. These studies suggest that TNFRSF14 dysregulation may contribute to the pathobiology of CHL in a subset of cases.
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- 2015
19. Mutations in SPAG1 Cause Primary Ciliary Dyskinesia Associated with Defective Outer and Inner Dynein Arms
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Whitney E. Wolf, Katrina A. Diaz, Edgar A. Otto, Rim Hjeij, Moumita Chaki, Niki T. Loges, Michael R. Knowles, Petra Pennekamp, Heike Olbrich, Lu Huang, Johanna Raidt, Jan Halbritter, Heon Yung Gee, Heymut Omran, Jay Shendure, Kenneth N. Olivier, Julia Wallmeier, Claudius Werner, Weining Yin, Friedhelm Hildebrandt, Jonathan D. Porath, Michael J. Bamshad, Toby W. Hurd, Matthias Griese, Alexandra P. Lewis, Emily H. Turner, Milan J. Hazucha, Johnny L. Carson, Gerard W. Dougherty, Gyorgy Baktai, Daniela A. Braun, Markus Schueler, Maimoona B Zariwala, Charlotte Jahnke, Thomas W. Ferkol, Sharon D. Dell, Lawrence E. Ostrowski, Margaret W. Leigh, Stephanie D. Davis, Scott D. Sagel, and Deborah A. Nickerson
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Adult ,Male ,Cytoplasm ,Axoneme ,Adolescent ,Dynein ,Biology ,medicine.disease_cause ,Young Adult ,03 medical and health sciences ,0302 clinical medicine ,GTP-Binding Proteins ,Report ,otorhinolaryngologic diseases ,Genetics ,medicine ,Animals ,Humans ,Genetics(clinical) ,Exome ,Cilia ,Child ,Zebrafish ,Genetics (clinical) ,Exome sequencing ,030304 developmental biology ,Primary ciliary dyskinesia ,0303 health sciences ,Mutation ,Kartagener Syndrome ,Cilium ,Dyneins ,Infant ,Epithelial Cells ,Inner dynein arm ,medicine.disease ,Pedigree ,Phenotype ,Child, Preschool ,030220 oncology & carcinogenesis ,Antigens, Surface ,Ciliary Motility Disorders ,Female - Abstract
Primary ciliary dyskinesia (PCD) is a genetically heterogeneous, autosomal-recessive disorder, characterized by oto-sino-pulmonary disease and situs abnormalities. PCD-causing mutations have been identified in 20 genes, but collectively they account for only ∼65% of all PCDs. To identify mutations in additional genes that cause PCD, we performed exome sequencing on three unrelated probands with ciliary outer and inner dynein arm (ODA+IDA) defects. Mutations in SPAG1 were identified in one family with three affected siblings. Further screening of SPAG1 in 98 unrelated affected individuals (62 with ODA+IDA defects, 35 with ODA defects, 1 without available ciliary ultrastructure) revealed biallelic loss-of-function mutations in 11 additional individuals (including one sib-pair). All 14 affected individuals with SPAG1 mutations had a characteristic PCD phenotype, including 8 with situs abnormalities. Additionally, all individuals with mutations who had defined ciliary ultrastructure had ODA+IDA defects. SPAG1 was present in human airway epithelial cell lysates but was not present in isolated axonemes, and immunofluorescence staining showed an absence of ODA and IDA proteins in cilia from an affected individual, thus indicating that SPAG1 probably plays a role in the cytoplasmic assembly and/or trafficking of the axonemal dynein arms. Zebrafish morpholino studies of spag1 produced cilia-related phenotypes previously reported for PCD-causing mutations in genes encoding cytoplasmic proteins. Together, these results demonstrate that mutations in SPAG1 cause PCD with ciliary ODA+IDA defects and that exome sequencing is useful to identify genetic causes of heterogeneous recessive disorders.
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- 2013
20. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
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Jacob O. Kitzman, Choli Lee, Jay Shendure, Joseph B. Hiatt, Alexandra P. Lewis, Andrew Adey, Beth Martin, Ruolan Qiu, and Joshua N. Burton
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Epigenomics ,Transcriptional Activation ,DNA Copy Number Variations ,Molecular Sequence Data ,Genes, myc ,Uterine Cervical Neoplasms ,Biology ,medicine.disease_cause ,Proto-Oncogene Mas ,Genome ,Gene dosage ,Article ,HeLa ,Loss of heterozygosity ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Humans ,Gene ,030304 developmental biology ,Genetics ,0303 health sciences ,Mutation ,Multidisciplinary ,Human papillomavirus 18 ,Genome, Human ,Sequence Analysis, DNA ,Aneuploidy ,biology.organism_classification ,3. Good health ,Haplotypes ,030220 oncology & carcinogenesis ,Female ,Human genome ,HeLa Cells ,Reference genome - Abstract
Haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain shows that HeLa is relatively stable in terms of point variation; integration of several data sets reveals strong, haplotype-specific activation of the proto-oncogene MYC by the human papilloma virus type 18 genome, and enables the relationship between gene dosage and expression to be examined. The first genomic characterization of the HeLa cancer cell line, the longest-serving and arguably most commonly used human cell line in biomedical research, reveals a genome that is surprisingly stable with respect to both point-mutation and copy-number alterations. The point-mutation rate may be no higher than the somatic mutation rate of normal tissue, and very few copy-number alterations distinguish the genomes of different HeLa strains that were split from one another in the mid-1950s. The authors examine the relationship between gene dosage and expression by integrating several data sets, including those from the ENCODE project, and find strong activation of the MYC proto-oncogene by the human papilloma virus type 18 (HPV-18) integration at chromosome 8q24.21. The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks. This was the first successful attempt to immortalize human-derived cells in vitro1. The robust growth and unrestricted distribution of HeLa cells resulted in its broad adoption—both intentionally and through widespread cross-contamination2—and for the past 60 years it has served a role analogous to that of a model organism3. The cumulative impact of the HeLa cell line on research is demonstrated by its occurrence in more than 74,000 PubMed abstracts (approximately 0.3%). The genomic architecture of HeLa remains largely unexplored beyond its karyotype4, partly because like many cancers, its extensive aneuploidy renders such analyses challenging. We carried out haplotype-resolved whole-genome sequencing5 of the HeLa CCL-2 strain, examined point- and indel-mutation variations, mapped copy-number variations and loss of heterozygosity regions, and phased variants across full chromosome arms. We also investigated variation and copy-number profiles for HeLa S3 and eight additional strains. We find that HeLa is relatively stable in terms of point variation, with few new mutations accumulating after early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24.21 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis. We combined these maps with RNA-seq6 and ENCODE Project7 data sets to phase the HeLa epigenome. This revealed strong, haplotype-specific activation of the proto-oncogene MYC by the integrated HPV-18 genome approximately 500 kilobases upstream, and enabled global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for characterizing cancer genomes and epigenomes.
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- 2013
21. Noninvasive whole-genome sequencing of a human fetus
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Jeffrey C. Murray, Donna A. Santillan, Alexandra P. Lewis, La Vone E Simmons, Holly K. Tabor, Craig E. Rubens, Jacob O. Kitzman, Michael J. Bamshad, Matthew W. Snyder, Evan E. Eichler, Ruolan Qiu, Hilary S. Gammill, Mario Ventura, and Jay Shendure
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Genetics ,Whole genome sequencing ,Haplotype ,High-Throughput Nucleotide Sequencing ,Prenatal diagnosis ,Gestational Age ,General Medicine ,DNA ,Biology ,Genome ,Deep sequencing ,DNA sequencing ,Article ,Fetus ,Cell-free fetal DNA ,Haplotypes ,Pregnancy ,Prenatal Diagnosis ,Humans ,Female ,Genotyping - Abstract
Analysis of cell-free fetal DNA in maternal plasma holds promise for the development of noninvasive prenatal genetic diagnostics. Previous studies have been restricted to detection of fetal trisomies, to specific paternally inherited mutations, or to genotyping common polymorphisms using material obtained invasively, for example, through chorionic villus sampling. Here, we combine genome sequencing of two parents, genome-wide maternal haplotyping, and deep sequencing of maternal plasma DNA to noninvasively determine the genome sequence of a human fetus at 18.5 weeks of gestation. Inheritance was predicted at 2.8 × 10(6) parental heterozygous sites with 98.1% accuracy. Furthermore, 39 of 44 de novo point mutations in the fetal genome were detected, albeit with limited specificity. Subsampling these data and analyzing a second family trio by the same approach indicate that parental haplotype blocks of ~300 kilo-base pairs combined with shallow sequencing of maternal plasma DNA is sufficient to substantially determine the inherited complement of a fetal genome. However, ultradeep sequencing of maternal plasma DNA is necessary for the practical detection of fetal de novo mutations genome-wide. Although technical and analytical challenges remain, we anticipate that noninvasive analysis of inherited variation and de novo mutations in fetal genomes will facilitate prenatal diagnosis of both recessive and dominant Mendelian disorders.
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- 2012
22. Non-invasive fetal genome sequencing: opportunities and challenges
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Jay Shendure, Mario Ventura, Holly K. Tabor, Craig E. Rubens, Edith Cheng, Jacob O. Kitzman, LaVone E. Simmons, Matthew W. Snyder, Michael J. Bamshad, Jeffrey C. Murray, Evan E. Eichler, Ruolan Qiu, Alexandra P. Lewis, Hilary S. Gammill, and Mark K. Santillan
- Subjects
medicine.medical_specialty ,Genetic counseling ,Population ,Psychological intervention ,Prenatal diagnosis ,Disease ,Prenatal care ,Article ,Pregnancy ,Prenatal Diagnosis ,Genetics ,Medicine ,Humans ,education ,Intensive care medicine ,Genetics (clinical) ,Genetic testing ,education.field_of_study ,medicine.diagnostic_test ,business.industry ,Genome, Human ,Sequence Analysis, DNA ,Fetal Diseases ,Female ,business ,Return of results - Abstract
We recently predicted the whole genome sequence of a human fetus using samples obtained non-invasively from the pregnant mother and the father. [Kitzman et al., 2012] This advance raises the possibility that it may soon be possible to perform genome-wide prenatal genetic testing without an invasive procedure early in pregnancy. Such a test would substantially broaden the scope of fetal genetic results that could be available prenatally. Non-invasive fetal genome sequencing (NIFGS) does not inherently raise new ethical issues, or those that cannot be addressed within the existing framework of medical bioethics. Indeed, many of the same issues have been raised by the introduction of other prenatal testing / screening technologies, now in wide use, and again more recently by the introduction of whole genome sequencing for clinical diagnosis. [Sayres et al., 2011, Schmitz et al., 2009, Ravitsky, 2009, Benn et al., 2009, Tabor et al., 2011, Berg et al., 2011] However, the ethical issues are, somewhat, magnified by the possibility of NIFGS and compounded by controversies surrounding elective pregnancy termination, rights of individuals with disabilities, and eugenics. Accordingly, the prospect of successful NIFGS, even on a research basis, is likely to generate considerable controversy and debate about the acceptability of developing such technologies, much less if and how they should be used. We view this response as very positive because it provides all stakeholders and the broader public in general with the opportunity to carefully consider and deliberate these issues in what we would hope is a thoughtful and balanced way. As NIFGS becomes technically tractable and increasingly cost-effective, and as an acceptable false positive/false negative profile is achieved, one population for which it might be of great benefit may be pregnant women who are currently offered invasive prenatal diagnostic testing. Such women are typically at risk for genetic conditions based on screening results or family history, and NIFGS would likely reduce if not eliminate adverse outcomes from invasive testing for most of these women. The expanded use of NIFGS would present several advantages and challenges. Broader use of NIFGS might lead to the greater detection of Mendelian disorders in families who would not otherwise have been offered prenatal testing, as well as families who might have refused invasive testing because of risks to the pregnancy and fetus. NIFGS could augment or even replace current approaches to neonatal screening as most such disorders are autosomal or X-linked recessive (e.g., hypothyroidism and congenital hearing loss are only sometimes Mendelian). Prenatal identification of disorders now found in neonatal screening would afford for earlier parental education, diminished false positives and the accompanying costs of retesting and parental anxiety and earlier therapeutic interventions. Earlier detection of such disorders would also foster improved prenatal care, pregnancy and delivery management and/or postnatal intervention. For example, 90% of genetic variants in SCNA1 that cause seizure disorders are de novo, and identification by NIFGS could allow for diagnosis before the onset of seizures and consideration of appropriate precautions and/or pharmacological treatment. [Marini et al., 20011] Similarly, 50% of mutations causing Multiple Endocrine Neoplasia 2B are spontaneous, and earlier identification of these mutations could prompt prophylactic thyroidectomy and improve outcomes. [Carlson et al., 1994] The availability of NIFGS could increase the utilization of prenatal testing, and in turn increase rates of elective termination, both for disorders for which testing is currently available and for the wide arrange of disorders and traits for which testing would be newly available. [Tischler et al., 2011] On the other hand, NIFGS might also make pregnancy termination safer, less costly, and less traumatic as it could be performed early in gestation. Broad use of NIFGS might result in increased societal pressure for pregnant women to undergo screening and terminate any fetus suspected to have a Mendelian condition. This could reverse important and continuing social progress towards civil rights and social support for people and families with disabilities. In addition, this societal pressure might threaten parental autonomy over reproductive decision-making. Broader use of NIFGS might also create or magnify social stigmas or inequities. NIFGS would likely remain expensive and may not be reimbursable by insurance in the short-term. This might exaggerate disparities between people who can easily afford access and those who cannot. If access is limited to those who can afford it, it is possible that a disproportionate number of lower income families could suffer from the higher rates of morbidity and mortality of invasive testing. In the extreme scenario, children with Mendelian conditions would be disproportionately born to lower income families that could not afford NIFGS. Such a disparity would likely further stigmatize many of these conditions and exaggerate existing disparities in access to healthcare and benefits for these populations. Another key issue raised by NIFGS is that it represents a substantially more comprehensive test for Mendelian disorders with a known cause, and will identify variants that are beyond the scope of conventional prenatal screening and diagnosis. Specifically, variants will be identified that indicate increased risk for developing adult onset conditions. This is not unique to NIFGS: in fact this is an ongoing challenge in pediatric clinical genetic testing. [Wilfond et al., 2009] Such information may be irrelevant or inappropriate to return for the benefit of the fetus/future child, but may have direct implications for the health of the parent, and therefore provide indirect benefit to any current or future children. However, if NIFGS is more broadly implemented, the scope of the results identified and the number of individuals affected may increase substantially. This will further overwhelm the existing infrastructure for providing genetic counseling. As with other applications of whole-genome sequencing, NIFGS will identify variants of ambiguous clinical utility in genes known to be associated with both pediatric and adult complex disease. For example, Kitzman et al. found a de novo novel missense variant in ACMSD, a gene in which common variants have been associated with Parkinson disease by genome-wide association. [Klitzman et al., 2012, International Parkinson Disease Genomics Consortium et al., 2011] This variant causes substitution of a highly conserved amino acid residue, but in the absence of compelling evidence of its role in Parkinson disease or other conditions, its detection is of limited clinical value. While this is no different than the challenge of interpreting WGS information in general, pregnancy might be a particularly vulnerable time in which to receive this information and parents might feel compelled to give more credence to the information than it warrants. There are several other important issues that require consideration. Will the non-invasive nature of this test, combined with the enhanced detection of Mendelian disorders, lead to a substantial increase in the number of women who consider prenatal diagnosis? How will the medical community meet the challenge of providing genetic counseling to address the complex nature of the information that may be identified? These concerns raise the possibility that some women may not be able to provide adequate informed consent, or may proceed with actions such as terminations without complete understanding of the test results or the prognosis for various rare Mendelian disorders. If NIFGS allows the creation of a record of a child’s whole genome prior to its birth, what should happen to that data? Should it be stored as part of the child’s medical record, with the possibility for future updating, analysis and mining for medically relevant information? Or should it be destroyed? Who should make this decision and have control over the data? As with many new technologies, NIFGS will be accompanied by many ethical and social challenges. We think that it is imperative that these questions and issues be discussed and addressed by a diverse group of stakeholders, as well as through collection of empirical data on stakeholder perspectives and concerns. Much can be learned from the history of the implementation of other prenatal testing approaches, such as amniocentesis and CVS, as well as the ongoing debates about pediatric genetic testing and return of results from whole genome sequencing. [Rapp, 2000]
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- 2012
23. General instruments for risk assessment.
- Author
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Alexandra H Lewis
- Abstract
PURPOSE OF REVIEW: The identification of those who may be at increased risk of exhibiting violence is one of the highest-profile tasks of mental health professionals. Risk assessment is a rapidly developing field, and a number of instruments have been proposed for facilitating this task.RECENT FINDINGS: This article summarizes the main developments in the field of risk assessment and examines the key themes that have emerged over the past year. It discusses recent findings concerning comparisons between risk-assessment instruments and ways of optimizing the predictive accuracy of risk-assessment tools. A trend over the past year has been that risk assessment has begun to be seen as a multi-disciplinary task rather than falling within the remit of a single professional group. Several papers in the past year have explored issues concerned with the practical application of risk-assessment instruments.SUMMARY: Risk-assessment instruments can play a valuable role in identifying those who may be at increased risk of exhibiting violent behaviour. However, they should be interpreted with caution rather than being regarded as fixed entities. Practitioners should be aware that all risk-assessment instruments are ‘works in progress’ and are likely to require ongoing revision. [ABSTRACT FROM AUTHOR]
- Published
- 2004
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24. Exome Sequencing Identifies Mutations in CCDC114 as a Cause of Primary Ciliary Dyskinesia
- Author
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Michael R, Knowles, Margaret W, Leigh, Lawrence E, Ostrowski, Lu, Huang, Johnny L, Carson, Milan J, Hazucha, Weining, Yin, Jonathan S, Berg, Stephanie D, Davis, Sharon D, Dell, Thomas W, Ferkol, Margaret, Rosenfeld, Scott D, Sagel, Carlos E, Milla, Kenneth N, Olivier, Emily H, Turner, Alexandra P, Lewis, Michael J, Bamshad, Deborah A, Nickerson, Jay, Shendure, Maimoona A, Zariwala, and Caroline, O'Connor
- Subjects
Proband ,Adult ,Male ,Genes, Recessive ,Biology ,medicine.disease_cause ,Bioinformatics ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Report ,medicine ,Genetics ,otorhinolaryngologic diseases ,Humans ,Protein Isoforms ,Genetics(clinical) ,Exome ,Genetics (clinical) ,Exome sequencing ,030304 developmental biology ,Primary ciliary dyskinesia ,Sanger sequencing ,0303 health sciences ,Mutation ,Genetic heterogeneity ,Kartagener Syndrome ,Sequence Analysis, DNA ,Middle Aged ,medicine.disease ,3. Good health ,Pedigree ,030228 respiratory system ,Child, Preschool ,symbols ,Female ,Outer dynein arm ,Microtubule-Associated Proteins - Abstract
Primary ciliary dyskinesia (PCD) is a genetically heterogeneous, autosomal-recessive disorder, characterized by oto-sino-pulmonary disease and situs abnormalities. PCD-causing mutations have been identified in 14 genes, but they collectively account for only ∼60% of all PCD. To identify mutations that cause PCD, we performed exome sequencing on six unrelated probands with ciliary outer dynein arm (ODA) defects. Mutations in CCDC114, an ortholog of the Chlamydomonas reinhardtii motility gene DCC2, were identified in a family with two affected siblings. Sanger sequencing of 67 additional individuals with PCD with ODA defects from 58 families revealed CCDC114 mutations in 4 individuals in 3 families. All 6 individuals with CCDC114 mutations had characteristic oto-sino-pulmonary disease, but none had situs abnormalities. In the remaining 5 individuals with PCD who underwent exome sequencing, we identified mutations in two genes (DNAI2, DNAH5) known to cause PCD, including an Ashkenazi Jewish founder mutation in DNAI2. These results revealed that mutations in CCDC114 are a cause of ciliary dysmotility and PCD and further demonstrate the utility of exome sequencing to identify genetic causes in heterogeneous recessive disorders.
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25. Whole genome prediction for preimplantation genetic diagnosis
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Nina M. Wemmer, Matthew Rabinowitz, Milena Banjevic, Jacob O. Kitzman, Choli Lee, Alexandra P. Lewis, Jay Shendure, Akash Kumar, Paul W. Zarutskie, Matthew W. Snyder, Styrmir Sigurjonsson, and Allison M. Ryan
- Subjects
Whole genome sequencing ,Genetics ,Preimplantation genetic haplotyping ,Research ,Biology ,Preimplantation genetic diagnosis ,Genome ,DNA sequencing ,Human genetics ,Single cell sequencing ,Molecular Medicine ,Genetics(clinical) ,Genotyping ,Molecular Biology ,Genetics (clinical) - Abstract
Background Preimplantation genetic diagnosis (PGD) enables profiling of embryos for genetic disorders prior to implantation. The majority of PGD testing is restricted in the scope of variants assayed or by the availability of extended family members. While recent advances in single cell sequencing show promise, they remain limited by bias in DNA amplification and the rapid turnaround time (
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