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2. Variants in genes coding for collagen type IV [alpha]-chains are frequent causes of persistent, isolated hematuria during childhood

Author

Alge, Joseph L., Bekheirnia, Nasim, Willcockson, Alexandra R., Qin, Xiang, Scherer, Steven E., Braun, Michael C., and Bekheirnia, Mir Reza

Subjects
Diagnosis, Care and treatment, Analysis, Usage, Health aspects, Collagen -- Usage -- Health aspects, DNA sequencing -- Analysis, Genetic variation -- Analysis, Hematuria -- Diagnosis -- Care and treatment, Nucleotide sequencing -- Analysis
Abstract

Author(s): Joseph L. Alge [sup.1] , Nasim Bekheirnia [sup.1] , Alexandra R. Willcockson [sup.2] , Xiang Qin [sup.3] , Steven E. Scherer [sup.3] [sup.4] , Michael C. Braun [sup.1] , [...], Background Children with persistent, isolated microscopic hematuria typically undergo a limited diagnostic workup and are monitored for signs of kidney disease in long-term longitudinal follow-up, which can delay diagnosis and allow disease progression in some cases. Methods To determine the clinical utility of genetic screening in this population, we performed targeted genetic testing using a custom, 32-gene next-generation sequencing panel for progressive kidney disease on children referred to the Texas Children's Hospital Pediatric Nephrology clinic for persistent, microscopic hematuria (n = 30; cohort 1). Patients with microscopic hematuria identified by urinalysis on at least two separate occasions were eligible for enrollment, but those with other evidence of kidney disease were excluded. Results were analyzed for sequence variants using the American College of Medical Genetics and Genomics (ACMG) guideline for data interpretation and were validated using a secondary analysis of a dataset of children with hematuria and normal kidney function who had undergone genetic testing as part of an industry-sponsored program (cohort 2; n = 67). Results In cohort 1 33% of subjects (10/30) had pathogenic or likely pathogenic (P/LP) variants in the type IV collagen genes (COL4A3/A4/A5), and 10% (3/30) had variants of uncertain significance in these genes. The high diagnostic rate in type IV collagen genes was confirmed in cohort 2, where 27% (18/67) of subjects had P/LP variants in COL4A3/A4/A5 genes. Conclusions Children with persistent, isolated microscopic hematuria have a high likelihood of having pathogenic variants in type IV collagen genes and genetic screening should be considered. Graphical Abstract

Published
2023
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3. Experiences in providing a community educational resource for the All of Us Researcher Workbench.

Author

Ritter, Deborah I, Byun, Jinyoung, Wang, Jun, Richards, Stephen, Luna, Pamela N, Williams, LaTerrica, Coleman, Julie R, Baker, Jasmine N, Ketkar, Shamika, Butler, Ashley M, Hammonds-Odie, Latanya, Atkinson, Elizabeth G, Worley, Kim C, Murray, Debra D, Lee, Brendan, and Scherer, Steven E

Abstract

Objective Educational offerings to fill the bioinformatics knowledge gap are a key component to enhancing access and use of health data from the All of Us Research Program. We developed a Train the Trainer-based, innovative training series including project-based learning, modular on-demand demonstrations, and unstructured tutorial time as a model for educational engagement in the All of Us community. Materials and Methods We highlight our training modules and content, with training survey data informing cycles of development in the creation of a 6-module training series with modular demonstrations. Results We have conducted 2 public iterations of the Train the Trainer (Tx3) Series based on survey feedback while training over 300 registered researchers to access and analyze data on the All of Us Researcher Workbench. Discussion and Conclusion Future directions of the Tx3 Series include enhanced focus on project-based learning and learner requests for modularity and asynchronous materials access. [ABSTRACT FROM AUTHOR]

Published
2024
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4. Implementation of preemptive DNA sequence–based pharmacogenomics testing across a large academic medical center: The Mayo-Baylor RIGHT 10K Study

Author

Wang, Liewei, Scherer, Steven E., Bielinski, Suzette J., Muzny, Donna M., Jones, Leila A., Black, John Logan, III, Moyer, Ann M., Giri, Jyothsna, Sharp, Richard R., Matey, Eric T., Wright, Jessica A., Oyen, Lance J., Nicholson, Wayne T., Wiepert, Mathieu, Sullard, Terri, Curry, Timothy B., Rohrer Vitek, Carolyn R., McAllister, Tammy M., St. Sauver, Jennifer L., Caraballo, Pedro J., Lazaridis, Konstantinos N., Venner, Eric, Qin, Xiang, Hu, Jianhong, Kovar, Christie L., Korchina, Viktoriya, Walker, Kimberly, Doddapaneni, HarshaVardhan, Wu, Tsung-Jung, Raj, Ritika, Denson, Shawn, Liu, Wen, Chandanavelli, Gauthami, Zhang, Lan, Wang, Qiaoyan, Kalra, Divya, Karow, Mary Beth, Harris, Kimberley J., Sicotte, Hugues, Peterson, Sandra E., Barthel, Amy E., Moore, Brenda E., Skierka, Jennifer M., Kluge, Michelle L., Kotzer, Katrina E., Kloke, Karen, Vander Pol, Jessica M., Marker, Heather, Sutton, Joseph A., Kekic, Adrijana, Ebenhoh, Ashley, Bierle, Dennis M., Schuh, Michael J., Grilli, Christopher, Erickson, Sara, Umbreit, Audrey, Ward, Leah, Crosby, Sheena, Nelson, Eric A., Levey, Sharon, Elliott, Michelle, Peters, Steve G., Pereira, Naveen, Frye, Mark, Shamoun, Fadi, Goetz, Matthew P., Kullo, Iftikhar J., Wermers, Robert, Anderson, Jan A., Formea, Christine M., El Melik, Razan M., Zeuli, John D., Herges, Joseph R., Krieger, Carrie A., Hoel, Robert W., Taraba, Jodi L., St. Thomas, Scott R., Absah, Imad, Bernard, Matthew E., Fink, Stephanie R., Gossard, Andrea, Grubbs, Pamela L., Jacobson, Therese M., Takahashi, Paul, Zehe, Sharon C., Buckles, Susan, Bumgardner, Michelle, Gallagher, Colette, Fee-Schroeder, Kelliann, Nicholas, Nichole R., Powers, Melody L., Ragab, Ahmed K., Richardson, Darcy M., Stai, Anthony, Wilson, Jaymi, Pacyna, Joel E., Olson, Janet E., Sutton, Erica J., Beck, Annika T., Horrow, Caroline, Kalari, Krishna R., Larson, Nicholas B., Liu, Hongfang, Wang, Liwei, Lopes, Guilherme S., Borah, Bijan J., Freimuth, Robert R., Zhu, Ye, Jacobson, Debra J., Hathcock, Matthew A., Armasu, Sebastian M., McGree, Michaela E., Jiang, Ruoxiang, Koep, Tyler H., Ross, Jason L., Hilden, Matthew G., Bosse, Kathleen, Ramey, Bronwyn, Searcy, Isabelle, Boerwinkle, Eric, Gibbs, Richard A., and Weinshilboum, Richard M.

Published
2022
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5. CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project

Author

Gaedigk, Andrea, Boone, Erin C., Scherer, Steven E., Lee, Seung-been, Numanagić, Ibrahim, Sahinalp, Cenk, Smith, Joshua D., McGee, Sean, Radhakrishnan, Aparna, Qin, Xiang, Wang, Wendy Y., Farrow, Emily G., Gonzaludo, Nina, Halpern, Aaron L., Nickerson, Deborah A., Miller, Neil A., Pratt, Victoria M., and Kalman, Lisa V.

Published
2022
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11. Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Author

Chen, Zhen-Xia, Sturgill, David, Qu, Jiaxin, Jiang, Huaiyang, Park, Soo, Boley, Nathan, Suzuki, Ana Maria, Fletcher, Anthony R, Plachetzki, David C, FitzGerald, Peter C, Artieri, Carlo G, Atallah, Joel, Barmina, Olga, Brown, James B, Blankenburg, Kerstin P, Clough, Emily, Dasgupta, Abhijit, Gubbala, Sai, Han, Yi, Jayaseelan, Joy C, Kalra, Divya, Kim, Yoo-Ah, Kovar, Christie L, Lee, Sandra L, Li, Mingmei, Malley, James D, Malone, John H, Mathew, Tittu, Mattiuzzo, Nicolas R, Munidasa, Mala, Muzny, Donna M, Ongeri, Fiona, Perales, Lora, Przytycka, Teresa M, Pu, Ling-Ling, Robinson, Garrett, Thornton, Rebecca L, Saada, Nehad, Scherer, Steven E, Smith, Harold E, Vinson, Charles, Warner, Crystal B, Worley, Kim C, Wu, Yuan-Qing, Zou, Xiaoyan, Cherbas, Peter, Kellis, Manolis, Eisen, Michael B, Piano, Fabio, Kionte, Karin, Fitch, David H, Sternberg, Paul W, Cutter, Asher D, Duff, Michael O, Hoskins, Roger A, Graveley, Brenton R, Gibbs, Richard A, Bickel, Peter J, Kopp, Artyom, Carninci, Piero, Celniker, Susan E, Oliver, Brian, and Richards, Stephen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Animals, Cluster Analysis, Computational Biology, Drosophila melanogaster, Evolution, Molecular, Exons, Female, Gene Expression Profiling, Genome, Insect, Humans, Male, Molecular Sequence Annotation, Nucleotide Motifs, Phylogeny, Position-Specific Scoring Matrices, Promoter Regions, Genetic, RNA Editing, RNA Splice Sites, RNA Splicing, Reproducibility of Results, Transcription Initiation Site, Transcriptome, Medical and Health Sciences, Bioinformatics
Abstract

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

Published
2014

12. Whole-Organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis

Author

Majewski, Tadeusz, Yao, Hui, Bondaruk, Jolanta, Chung, Woonbok, Lee, Sangkyou, Lee, June Goo, Zhang, Shizhen, Cogdell, David, Yang, Guoliang, Choi, Woonyoung, Dinney, Colin, Grossman, H. Barton, Logothetis, Christopher, Scherer, Steven E., Guo, Charles C., Zhang, Li, Wei, Peng, Weinstein, John N., Issa, Jean-Pierre, Baggerly, Keith, McConkey, David J., and Czerniak, Bogdan

Published
2019
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13. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

Author

Chipman, Ariel D, Ferrier, David EK, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel ST, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer CJ, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis JP, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome HL, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, and Zou, Xiaoyan

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Prevention, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Arthropods, Circadian Rhythm Signaling Peptides and Proteins, DNA Methylation, Evolution, Molecular, Female, Genome, Genome, Mitochondrial, Hormones, Male, Multigene Family, Phylogeny, Polymorphism, Genetic, Protein Kinases, RNA, Untranslated, Receptors, Odorant, Selenoproteins, Sex Chromosomes, Synteny, Transcription Factors, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.

Published
2014

14. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

Author

Dasmahapatra, Kanchon K, Walters, James R, Briscoe, Adriana D, Davey, John W, Whibley, Annabel, Nadeau, Nicola J, Zimin, Aleksey V, Hughes, Daniel ST, Ferguson, Laura C, Martin, Simon H, Salazar, Camilo, Lewis, James J, Adler, Sebastian, Ahn, Seung-Joon, Baker, Dean A, Baxter, Simon W, Chamberlain, Nicola L, Chauhan, Ritika, Counterman, Brian A, Dalmay, Tamas, Gilbert, Lawrence E, Gordon, Karl, Heckel, David G, Hines, Heather M, Hoff, Katharina J, Holland, Peter WH, Jacquin-Joly, Emmanuelle, Jiggins, Francis M, Jones, Robert T, Kapan, Durrell D, Kersey, Paul, Lamas, Gerardo, Lawson, Daniel, Mapleson, Daniel, Maroja, Luana S, Martin, Arnaud, Moxon, Simon, Palmer, William J, Papa, Riccardo, Papanicolaou, Alexie, Pauchet, Yannick, Ray, David A, Rosser, Neil, Salzberg, Steven L, Supple, Megan A, Surridge, Alison, Tenger-Trolander, Ayse, Vogel, Heiko, Wilkinson, Paul A, Wilson, Derek, Yorke, James A, Yuan, Furong, Balmuth, Alexi L, Eland, Cathlene, Gharbi, Karim, Thomson, Marian, Gibbs, Richard A, Han, Yi, Jayaseelan, Joy C, Kovar, Christie, Mathew, Tittu, Muzny, Donna M, Ongeri, Fiona, Pu, Ling-Ling, Qu, Jiaxin, Thornton, Rebecca L, Worley, Kim C, Wu, Yuan-Qing, Linares, Mauricio, Blaxter, Mark L, Ffrench-Constant, Richard H, Joron, Mathieu, Kronforst, Marcus R, Mullen, Sean P, Reed, Robert D, Scherer, Steven E, Richards, Stephen, Mallet, James, McMillan, W Owen, and Jiggins, Chris D

Subjects
Adaptation, Physiological, Animals, Bombyx, Butterflies, Chromosomes, Insect, Evolution, Molecular, Gene Flow, Genes, Homeobox, Genes, Insect, Genome, Insect, Genomics, Hybridization, Genetic, Molecular Mimicry, Molecular Sequence Data, Phylogeny, Pigmentation, Sequence Analysis, DNA, Species Specificity, Synteny, Wings, Animal, Heliconius Genome Consortium, General Science & Technology
Abstract

The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.

Published
2012

15. A BAC-Based Physical Map of the Major Autosomes of Drosophila melanogaster

Author

Hoskins, Roger A., Nelson, Catherine R., Berman, Benjamin P., Laverty, Todd R., George, Reed A., Ciesiolka, Lisa, Naeemuddin, Mohammed, Arenson, Andrew D., Durbin, James, David, Robert G., Tabor, Paul E., Bailey, Michael R., DeShazo, Denise R., Catanese, Joseph, Mammoser, Aaron, Osoegawa, Kazutoyo, de Jong, Pieter J., Celniker, Susan E., Gibbs, Richard A., Rubin, Gerald M., and Scherer, Steven E.

Published
2000

16. The Genome Sequence of Drosophila melanogaster

Author

Adams, Mark D., Celniker, Susan E., Holt, Robert A., Evans, Cheryl A., Gocayne, Jeannine D., Amanatides, Peter G., Scherer, Steven E., Li, Peter W., Hoskins, Roger A., Galle, Richard F., George, Reed A., Lewis, Suzanna E., Richards, Stephen, Ashburner, Michael, Henderson, Scott N., Sutton, Granger G., Wortman, Jennifer R., Yandell, Mark D., Zhang, Qing, Chen, Lin X., Brandon, Rhonda C., Rogers, Yu-Hui C., Blazej, Robert G., Champe, Mark, Pfeiffer, Barret D., Wan, Kenneth H., Doyle, Clare, Baxter, Evan G., Helt, Gregg, Nelson, Catherine R., Abril, Josep F., Agbayani, Anna, An, Hui-Jin, Andrews-Pfannkoch, Cynthia, Baldwin, Danita, Ballew, Richard M., Basu, Anand, Baxendale, James, Bayraktaroglu, Leyla, Beasley, Ellen M., Beeson, Karen Y., Benos, P. V., Berman, Benjamin P., Bhandari, Deepali, Bolshakov, Slava, Borkova, Dana, Botchan, Michael R., Bouck, John, Brokstein, Peter, Brottier, Phillipe, Burtis, Kenneth C., Busam, Dana A., Butler, Heather, Cadieu, Edouard, Chandra, Ishwar, Cherry, J. Michael, Cawley, Simon, Dahlke, Carl, Davenport, Lionel B., Davies, Peter, de Pablos, Beatriz, Delcher, Arthur, Deng, Zuoming, Mays, Anne Deslattes, Dew, Ian, Dietz, Suzanne M., Dodson, Kristina, Doup, Lisa E., Downes, Michael, Dugan-Rocha, Shannon, Dunkov, Boris C., Dunn, Patrick, Durbin, Kenneth J., Evangelista, Carlos C., Ferraz, Concepcion, Ferriera, Steven, Fleischmann, Wolfgang, Fosler, Carl, Gabrielian, Andrei E., Garg, Neha S., Gelbart, William M., Glasser, Ken, Glodek, Anna, Gong, Fangcheng, Gorrell, J. Harley, Gu, Zhiping, Guan, Ping, Harris, Michael, Harris, Nomi L., Harvey, Damon, Heiman, Thomas J., Hernandez, Judith R., Houck, Jarrett, Hostin, Damon, Houston, Kathryn A., Howland, Timothy J., Wei, Ming-Hui, Ibegwam, Chinyere, Jalali, Mena, Kalush, Francis, Karpen, Gary H., Ke, Zhaoxi, Kennison, James A., Ketchum, Karen A., Kimmel, Bruce E., Kodira, Chinnappa D., Kraft, Cheryl, Kravitz, Saul, Kulp, David, Lai, Zhongwu, Lasko, Paul, Lei, Yiding, Levitsky, Alexander A., Li, Jiayin, Li, Zhenya, Liang, Yong, Lin, Xiaoying, Liu, Xiangjun, Mattei, Bettina, McIntosh, Tina C., McLeod, Michael P., McPherson, Duncan, Merkulov, Gennady, Milshina, Natalia V., Mobarry, Clark, Morris, Joe, Moshrefi, Ali, Mount, Stephen M., Moy, Mee, Murphy, Brian, Murphy, Lee, Muzny, Donna M., Nelson, David L., Nelson, David R., Nelson, Keith A., Nixon, Katherine, Nusskern, Deborah R., Pacleb, Joanne M., Palazzolo, Michael, Pittman, Gjange S., Pan, Sue, Pollard, John, Puri, Vinita, Reese, Martin G., Reinert, Knut, Remington, Karin, Scheeler, Frederick, Shen, Hua, Shue, Bixiang Christopher, Sidén-Kiamos, Inga, Simpson, Michael, Skupski, Marian P., Smith, Tom, Spier, Eugene, Spradling, Allan C., Stapleton, Mark, Strong, Renee, Sun, Eric, Svirskas, Robert, Tector, Cyndee, Turner, Russell, Venter, Eli, Wang, Aihui H., Wang, Xin, Wang, Zhen-Yuan, Wassarman, David A., Weinstock, George M., Weissenbach, Jean, Williams, Sherita M., Woodage, Trevor, Worley, Kim C., Wu, David, Yang, Song, Yao, Q. Alison, Ye, Jane, Yeh, Ru-Fang, Zaveri, Jayshree S., Zhan, Ming, Zhang, Guangren, Zhao, Qi, Zheng, Liansheng, Zheng, Xiangqun H., Zhong, Fei N., Zhong, Wenyan, Zhou, Xiaojun, Zhu, Shiaoping, Zhu, Xiaohong, Smith, Hamilton O., Gibbs, Richard A., Myers, Eugene W., Rubin, Gerald M., and Venter, J. Craig

Published
2000

17. Comparative genome sequencing of drosophila pseudoobscura: Chromosomal, gene and cis-element evolution

Author

Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, Thornton, Kevin, Todd, Melissa J., Chen, Rui, Meisel, Richard P., Couronne, Olivier, Hua, Sujun, Smith, Mark A., Bussemaker, Harmen J., van Batenburg, Marinus F., Howells, Sally L., Scherer, Steven E., Sodergren, Erica, Matthews, Beverly B., Crosby, Madeline A., Schroeder, Andrew J., Ortiz-Barrientos, Daniel, Rives, Catherine M., Metzker, Michael L., Muzny, Donna M., Scott, Graham, Steffen, David, Wheeler, David A., Worley, Kim C., Havlak, Paul, Durbin, K. James, Egan, Amy, Gill, Rachel, Hume, Jennifer, Morgan, Margaret B., Miner, George, Hamilton, Cerissa, Huang, Yanmei, Waldron, Lenee, Verduzco, Daniel, Blankenburg, Kerstin P., Dubchak, Inna, Noor, Mohamed A.F., Anderson, Wyatt, White, Kevin P., Clark, Andrew G., Schaeffer, Stephen W., Gelbart, William, Weinstock, George M., and Gibbs, Richard A.

Subjects
Applied life sciences
Abstract

The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have remained on the same arm, but within each arm gene order has been extensively reshuffled leading to the identification of approximately 1300 syntenic blocks. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 35 My since divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome wide average consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than control sequences between the species but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a picture of repeat mediated chromosomal rearrangement, and high co-adaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

Published
2004

18. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta

Author

Kanost, Michael R., Arrese, Estela L., Cao, Xiaolong, Chen, Yun-Ru, Chellapilla, Sanjay, Goldsmith, Marian R., Grosse-Wilde, Ewald, Heckel, David G., Herndon, Nicolae, Jiang, Haobo, Papanicolaou, Alexie, Qu, Jiaxin, Soulages, Jose L., Vogel, Heiko, Walters, James, Waterhouse, Robert M., Ahn, Seung-Joon, Almeida, Francisca C., An, Chunju, Aqrawi, Peshtewani, Bretschneider, Anne, Bryant, William B., Bucks, Sascha, Chao, Hsu, Chevignon, Germain, Christen, Jayne M., Clarke, David F., Dittmer, Neal T., Ferguson, Laura C.F., Garavelou, Spyridoula, Gordon, Karl H.J., Gunaratna, Ramesh T., Han, Yi, Hauser, Frank, He, Yan, Heidel-Fischer, Hanna, Hirsh, Ariana, Hu, Yingxia, Jiang, Hongbo, Kalra, Divya, Klinner, Christian, König, Christopher, Kovar, Christie, Kroll, Ashley R., Kuwar, Suyog S., Lee, Sandy L., Lehman, Rüdiger, Li, Kai, Li, Zhaofei, Liang, Hanquan, Lovelace, Shanna, Lu, Zhiqiang, Mansfield, Jennifer H., McCulloch, Kyle J., Mathew, Tittu, Morton, Brian, Muzny, Donna M., Neunemann, David, Ongeri, Fiona, Pauchet, Yannick, Pu, Ling-Ling, Pyrousis, Ioannis, Rao, Xiang-Jun, Redding, Amanda, Roesel, Charles, Sanchez-Gracia, Alejandro, Schaack, Sarah, Shukla, Aditi, Tetreau, Guillaume, Wang, Yang, Xiong, Guang-Hua, Traut, Walther, Walsh, Tom K., Worley, Kim C., Wu, Di, Wu, Wenbi, Wu, Yuan-Qing, Zhang, Xiufeng, Zou, Zhen, Zucker, Hannah, Briscoe, Adriana D., Burmester, Thorsten, Clem, Rollie J., Feyereisen, René, Grimmelikhuijzen, Cornelis J.P., Hamodrakas, Stavros J., Hansson, Bill S., Huguet, Elisabeth, Jermiin, Lars S., Lan, Que, Lehman, Herman K., Lorenzen, Marce, Merzendorfer, Hans, Michalopoulos, Ioannis, Morton, David B., Muthukrishnan, Subbaratnam, Oakeshott, John G., Palmer, Will, Park, Yoonseong, Passarelli, A. Lorena, Rozas, Julio, Schwartz, Lawrence M., Smith, Wendy, Southgate, Agnes, Vilcinskas, Andreas, Vogt, Richard, Wang, Ping, Werren, John, Yu, Xiao-Qiang, Zhou, Jing-Jiang, Brown, Susan J., Scherer, Steven E., Richards, Stephen, and Blissard, Gary W.

Published
2016
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19. Genomic analysis of two phlebotomine sand fly vectors of leishmania from the new and old World

Author

Labbe, Frederic, Abdeladhim, Maha, Abrudan, Jenica, Araki, Alejandra Saori, Araujo, Ricardo N., Arensburger, Peter, Benoit, Joshua B., Brazil, Reginaldo Pecanha, Bruno, Rafaela V., Rivas, Gustavo Bueno da Silva D. S., de Abreu, Vinicius Carvalho, Charamis, Jason, Coutinho-Abreu, Iliano V., da Costa-Latge, Samara G., Darby, Alistair, Dillon, Viv M., Emrich, Scott J., Fernandez-Medina, Daniela, Gontijo, Nelder Figueiredo, Flanley, Catherine M., Gatherer, Derek, Genta, Fernando A., Gesing, Sandra, Giraldo-Calderon, Gloria I., Gomes, Bruno, Aguiar, Eric Roberto Guimaraes Rocha, Hamilton, James GC C., Hamarsheh, Omar, Hawksworth, Mallory, Hendershot, Jacob M., Hickner, Paul V., Imler, Jean-Luc, Ioannidis, Panagiotis, Jennings, Emily C., Kamhawi, Shaden, Karageorgiou, Charikleia, Kennedy, Ryan C., Krueger, Andreas, Latorre-Estivalis, Jose M., Ligoxygakis, Petros, Meireles-Filho, Antonio Carlos A., Minx, Patrick, Miranda, Jose Carlos, Montague, Michael J., Nowling, Ronald J., Oliveira, Fabiano, Ortigao-Farias, Joao, Pavan, Marcio G., Pereira, Marcos Horacio, Pitaluga, Andre Nobrega, Olmo, Roenick Proveti, Ramalho-Ortigao, Marcelo, Ribeiro, Jose MC C., Rosendale, Andrew J., Sant'Anna, Mauricio RV V., Scherer, Steven E., Secundino, Nagila FC C., Shoue, Douglas A., Moraes, Caroline da Silva D. S., Gesto, Joao Silveira Moledo, Souza, Nataly Araujo, Syed, Zainulabueddin, Tadros, Samuel, Teles-de-Freitas, Rayane, Telleria, Erich L., Tomlinson, Chad, Traub-Cseko, Yara M., Marques, Joao Trindade, Tu, Zhijian, Unger, Maria F., Valenzuela, Jesus, Ferreira, Flavia, de Oliveira, Karla PV V., Vigoder, Felipe M., Vontas, John, Wang, Lihui, Weedall, Gareth D., Zhioua, Elyes, Richards, Stephen, Warren, Wesley C., Waterhouse, Robert M., Dillon, Rod J., McDowell, Mary Ann, Labbe, Frederic, Abdeladhim, Maha, Abrudan, Jenica, Araki, Alejandra Saori, Araujo, Ricardo N., Arensburger, Peter, Benoit, Joshua B., Brazil, Reginaldo Pecanha, Bruno, Rafaela V., Rivas, Gustavo Bueno da Silva D. S., de Abreu, Vinicius Carvalho, Charamis, Jason, Coutinho-Abreu, Iliano V., da Costa-Latge, Samara G., Darby, Alistair, Dillon, Viv M., Emrich, Scott J., Fernandez-Medina, Daniela, Gontijo, Nelder Figueiredo, Flanley, Catherine M., Gatherer, Derek, Genta, Fernando A., Gesing, Sandra, Giraldo-Calderon, Gloria I., Gomes, Bruno, Aguiar, Eric Roberto Guimaraes Rocha, Hamilton, James GC C., Hamarsheh, Omar, Hawksworth, Mallory, Hendershot, Jacob M., Hickner, Paul V., Imler, Jean-Luc, Ioannidis, Panagiotis, Jennings, Emily C., Kamhawi, Shaden, Karageorgiou, Charikleia, Kennedy, Ryan C., Krueger, Andreas, Latorre-Estivalis, Jose M., Ligoxygakis, Petros, Meireles-Filho, Antonio Carlos A., Minx, Patrick, Miranda, Jose Carlos, Montague, Michael J., Nowling, Ronald J., Oliveira, Fabiano, Ortigao-Farias, Joao, Pavan, Marcio G., Pereira, Marcos Horacio, Pitaluga, Andre Nobrega, Olmo, Roenick Proveti, Ramalho-Ortigao, Marcelo, Ribeiro, Jose MC C., Rosendale, Andrew J., Sant'Anna, Mauricio RV V., Scherer, Steven E., Secundino, Nagila FC C., Shoue, Douglas A., Moraes, Caroline da Silva D. S., Gesto, Joao Silveira Moledo, Souza, Nataly Araujo, Syed, Zainulabueddin, Tadros, Samuel, Teles-de-Freitas, Rayane, Telleria, Erich L., Tomlinson, Chad, Traub-Cseko, Yara M., Marques, Joao Trindade, Tu, Zhijian, Unger, Maria F., Valenzuela, Jesus, Ferreira, Flavia, de Oliveira, Karla PV V., Vigoder, Felipe M., Vontas, John, Wang, Lihui, Weedall, Gareth D., Zhioua, Elyes, Richards, Stephen, Warren, Wesley C., Waterhouse, Robert M., Dillon, Rod J., and McDowell, Mary Ann

Abstract

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.

Published
2023

20. Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World

Author

Labbé, Frédéric, primary, Abdeladhim, Maha, additional, Abrudan, Jenica, additional, Araki, Alejandra Saori, additional, Araujo, Ricardo N., additional, Arensburger, Peter, additional, Benoit, Joshua B., additional, Brazil, Reginaldo Pecanha, additional, Bruno, Rafaela V., additional, Bueno da Silva Rivas, Gustavo, additional, Carvalho de Abreu, Vinicius, additional, Charamis, Jason, additional, Coutinho-Abreu, Iliano V., additional, da Costa-Latgé, Samara G., additional, Darby, Alistair, additional, Dillon, Viv M., additional, Emrich, Scott J., additional, Fernandez-Medina, Daniela, additional, Figueiredo Gontijo, Nelder, additional, Flanley, Catherine M., additional, Gatherer, Derek, additional, Genta, Fernando A., additional, Gesing, Sandra, additional, Giraldo-Calderón, Gloria I., additional, Gomes, Bruno, additional, Aguiar, Eric Roberto Guimaraes Rocha, additional, Hamilton, James G. C., additional, Hamarsheh, Omar, additional, Hawksworth, Mallory, additional, Hendershot, Jacob M., additional, Hickner, Paul V., additional, Imler, Jean-Luc, additional, Ioannidis, Panagiotis, additional, Jennings, Emily C., additional, Kamhawi, Shaden, additional, Karageorgiou, Charikleia, additional, Kennedy, Ryan C., additional, Krueger, Andreas, additional, Latorre-Estivalis, José M., additional, Ligoxygakis, Petros, additional, Meireles-Filho, Antonio Carlos A., additional, Minx, Patrick, additional, Miranda, Jose Carlos, additional, Montague, Michael J., additional, Nowling, Ronald J., additional, Oliveira, Fabiano, additional, Ortigão-Farias, João, additional, Pavan, Marcio G., additional, Horacio Pereira, Marcos, additional, Nobrega Pitaluga, Andre, additional, Proveti Olmo, Roenick, additional, Ramalho-Ortigao, Marcelo, additional, Ribeiro, José M. C., additional, Rosendale, Andrew J., additional, Sant’Anna, Mauricio R. V., additional, Scherer, Steven E., additional, Secundino, Nágila F. C., additional, Shoue, Douglas A., additional, da Silva Moraes, Caroline, additional, Gesto, João Silveira Moledo, additional, Souza, Nataly Araujo, additional, Syed, Zainulabueddin, additional, Tadros, Samuel, additional, Teles-de-Freitas, Rayane, additional, Telleria, Erich L., additional, Tomlinson, Chad, additional, Traub-Csekö, Yara M., additional, Marques, João Trindade, additional, Tu, Zhijian, additional, Unger, Maria F., additional, Valenzuela, Jesus, additional, Ferreira, Flávia V., additional, de Oliveira, Karla P. V., additional, Vigoder, Felipe M., additional, Vontas, John, additional, Wang, Lihui, additional, Weedall, Gareth D., additional, Zhioua, Elyes, additional, Richards, Stephen, additional, Warren, Wesley C., additional, Waterhouse, Robert M., additional, Dillon, Rod J., additional, and McDowell, Mary Ann, additional

Published
2023
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21. Supplementary Figure Legends 1-6 from High Frequency of PIK3R1 and PIK3R2 Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability

Author

Cheung, Lydia W.T., primary, Hennessy, Bryan T., primary, Li, Jie, primary, Yu, Shuangxing, primary, Myers, Andrea P., primary, Djordjevic, Bojana, primary, Lu, Yiling, primary, Stemke-Hale, Katherine, primary, Dyer, Mary D., primary, Zhang, Fan, primary, Ju, Zhenlin, primary, Cantley, Lewis C., primary, Scherer, Steven E., primary, Liang, Han, primary, Lu, Karen H., primary, Broaddus, Russell R., primary, and Mills, Gordon B., primary

Published
2023
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22. Data from High Frequency of PIK3R1 and PIK3R2 Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability

Author

Cheung, Lydia W.T., primary, Hennessy, Bryan T., primary, Li, Jie, primary, Yu, Shuangxing, primary, Myers, Andrea P., primary, Djordjevic, Bojana, primary, Lu, Yiling, primary, Stemke-Hale, Katherine, primary, Dyer, Mary D., primary, Zhang, Fan, primary, Ju, Zhenlin, primary, Cantley, Lewis C., primary, Scherer, Steven E., primary, Liang, Han, primary, Lu, Karen H., primary, Broaddus, Russell R., primary, and Mills, Gordon B., primary

Published
2023
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23. Supplementary Tables 1-3 from High Frequency of PIK3R1 and PIK3R2 Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability

Author

Cheung, Lydia W.T., primary, Hennessy, Bryan T., primary, Li, Jie, primary, Yu, Shuangxing, primary, Myers, Andrea P., primary, Djordjevic, Bojana, primary, Lu, Yiling, primary, Stemke-Hale, Katherine, primary, Dyer, Mary D., primary, Zhang, Fan, primary, Ju, Zhenlin, primary, Cantley, Lewis C., primary, Scherer, Steven E., primary, Liang, Han, primary, Lu, Karen H., primary, Broaddus, Russell R., primary, and Mills, Gordon B., primary

Published
2023
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24. Supplementary Materials and Methods from High Frequency of PIK3R1 and PIK3R2 Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability

Author

Cheung, Lydia W.T., primary, Hennessy, Bryan T., primary, Li, Jie, primary, Yu, Shuangxing, primary, Myers, Andrea P., primary, Djordjevic, Bojana, primary, Lu, Yiling, primary, Stemke-Hale, Katherine, primary, Dyer, Mary D., primary, Zhang, Fan, primary, Ju, Zhenlin, primary, Cantley, Lewis C., primary, Scherer, Steven E., primary, Liang, Han, primary, Lu, Karen H., primary, Broaddus, Russell R., primary, and Mills, Gordon B., primary

Published
2023
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25. Supplementary Figures 1-6 from High Frequency of PIK3R1 and PIK3R2 Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability

Author

Cheung, Lydia W.T., primary, Hennessy, Bryan T., primary, Li, Jie, primary, Yu, Shuangxing, primary, Myers, Andrea P., primary, Djordjevic, Bojana, primary, Lu, Yiling, primary, Stemke-Hale, Katherine, primary, Dyer, Mary D., primary, Zhang, Fan, primary, Ju, Zhenlin, primary, Cantley, Lewis C., primary, Scherer, Steven E., primary, Liang, Han, primary, Lu, Karen H., primary, Broaddus, Russell R., primary, and Mills, Gordon B., primary

Published
2023
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26. Interview with Dr. Cheung from High Frequency of PIK3R1 and PIK3R2 Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability

Author

Cheung, Lydia W.T., primary, Hennessy, Bryan T., primary, Li, Jie, primary, Yu, Shuangxing, primary, Myers, Andrea P., primary, Djordjevic, Bojana, primary, Lu, Yiling, primary, Stemke-Hale, Katherine, primary, Dyer, Mary D., primary, Zhang, Fan, primary, Ju, Zhenlin, primary, Cantley, Lewis C., primary, Scherer, Steven E., primary, Liang, Han, primary, Lu, Karen H., primary, Broaddus, Russell R., primary, and Mills, Gordon B., primary

Published
2023
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28. Genomic Analysis of Two Phlebotomine Sand Fly Vectors ofLeishmaniafrom the New and Old World

Author

Labbé, Frédéric, primary, Abdeladhim, Maha, additional, Abrudan, Jenica, additional, Araki, Alejandra Saori, additional, Araujo, Ricardo N., additional, Arensburger, Peter, additional, Benoit, Joshua B., additional, Brazil, Reginaldo Pecanha, additional, Bruno, Rafaela V., additional, da Silva Rivas, Gustavo Bueno, additional, de Abreu, Vinicius Carvalho, additional, Charamis, Jason, additional, Coutinho-Abreu, Iliano V., additional, da Costa-Latgé, Samara G., additional, Darby, Alistair, additional, Dillon, Viv M., additional, Emrich, Scott, additional, Fernandez-Medina, Daniela, additional, Gontijo, Nelder Figueiredo, additional, Flannley, Catherine M., additional, Gatherer, Derek, additional, Genta, Fernando A., additional, Gesing, Sandra, additional, Giraldo-Calderón, Gloria I., additional, Gomes, Bruno, additional, Rocha Aguiar, Eric Roberto Guimaraes, additional, Hamarsheh, Omar, additional, Hawksworth, Mallory, additional, Hendershot, Jacob M., additional, Hickner, Paul V., additional, Imler, Jean-Luc, additional, Ioannidis, Panagiotis, additional, Jennings, Emily C., additional, Kamhawi, Shaden, additional, Karageorgiou, Charikleia, additional, Kennedy, Ryan C., additional, Krueger, Andreas, additional, Latorre-Estivalis, José M, additional, Ligoxgakis, Petros, additional, Meireles-Filho, Antonio Carlos A., additional, Miranda, Jose Carlos, additional, Montague, Michael, additional, Nowling, Ronald J., additional, Oliveira, Fabiano, additional, Ortigão-Farias, João, additional, Pavan, Marcio G., additional, Pereira, Marcos Horacio, additional, Pitaluga, Andre Nobrega, additional, Olmo, Roenick Proveti, additional, Ramalho-Ortigao, Marcelo, additional, Ribeiro, Jose Marcos, additional, Rosendale, Andrew J., additional, Sant’Anna, Mauricio R.V., additional, Scherer, Steven E., additional, Secundino, Nagila F. C., additional, Shoue, Douglas A., additional, da Silva Moraes, Caroline, additional, Moledo Gesto, João Silveira, additional, Souza, Nataly Araujo, additional, Syed, Zainulabueddin, additional, Tadros, Samuel, additional, Teles-de-Freitas, Rayane, additional, Telleria, Erich L., additional, Tomlinson, Chad, additional, Traub-Cseko, Yara, additional, Marques, João Trindade, additional, Tu, Zhijian, additional, Unger, Maria F, additional, Valenzuela, Jesus, additional, Ferreira, Flavia Viana, additional, de Oliveira, Karla Pollyanna Vieira, additional, Vigoder, Felipe M, additional, Vontas, John, additional, Wang, Lihui, additional, Weedel, Gareth, additional, Zhioua, Elyes, additional, Richards, Stephen, additional, Warren, Wesley C, additional, Waterhouse, Robert M., additional, Dillon, Rod J., additional, and McDowell, Mary Ann, additional

Published
2022
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29. Recurring germline mosaicism in a family due to reversion of an inherited derivative chromosome 8 from an 8;21 translocation with interstitial telomeric sequences

Author

Bi, Weimin, primary, Yuan, Bo, additional, Liu, Pengfei, additional, Murry, Jaclyn B, additional, Qin, Xiang, additional, Xia, Fan, additional, Quach, Thao, additional, Cooper, Lance M, additional, Wiszniewska, Joanna, additional, Hixson, Patricia, additional, Peacock, Sandra, additional, Tonk, Vijay S, additional, Huff, Robert W, additional, Ortega, Veronica, additional, Lupski, James R, additional, Scherer, Steven E, additional, Littlejohn, Rebecca Okashah, additional, Velagaleti, Gopalrao V N, additional, Roeder, Elizabeth R, additional, and Cheung, Sau Wai, additional

Published
2022
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32. Recurring germline mosaicism in a family due to reversion of an inherited derivative chromosome 8 from an 8;21 translocation with interstitial telomeric sequences.

Author

Weimin Bi, Bo Yuan, Pengfei Liu, Murry, Jaclyn B., Xiang Qin, Fan Xia, Thao Quach, Cooper, Lance M., Wiszniewska, Joanna, Hixson, Patricia, Peacock, Sandra, Tonk, Vijay S., Huff, Robert W., Ortega, Veronica, Lupski, James R., Scherer, Steven E., Littlejohn, Rebecca Okashah, Velagaleti, Gopalrao V. N., Roeder, Elizabeth R., and Sau Wai Cheung

Abstract

Background: Mosaicism for chromosomal structural abnormalities, other than marker or ring chromosomes, is rarely inherited. Methods: We performed cytogenetics studies and breakpoint analyses on a family with transmission of mosaicism for a derivative chromosome 8 (der(8)), resulting from an unbalanced translocation between the long arms of chromosomes 8 and 21 over three generations. Results: The proband and his maternal half-sister had mosaicism for a der(8) cell line leading to trisomy of the distal 21q, and both had Down syndrome phenotypic features. Mosaicism for a cell line with the der(8) and a normal cell line was also detected in a maternal half-cousin. The der(8) was inherited from the maternal grandmother who had four abnormal cell lines containing the der(8), in addition to a normal cell line. One maternal half-aunt had the der(8) and an isodicentric chromosome 21 (idic(21)). Sequencing studies revealed microhomologies at the junctures of the der(8) and idic(21) in the half-aunt, suggesting a replicative mechanism in the rearrangement formation. Furthermore, interstitial telomeric sequences (ITS) were identified in the juncture between chromosomes 8 and 21 in the der(8). Conclusion: Mosaicism in the proband, his half-sister and half-cousin resulting from loss of chromosome 21 material from the der(8) appears to be a postzygotic event due to the genomic instability of ITS and associated with selective growth advantage of normal cells. The reversion of the inherited der(8) to a normal chromosome 8 in this family resembles revertant mosaicism of point mutations. We propose that ITS could mediate recurring revertant mosaicism for some constitutional chromosomal structural abnormalities. [ABSTRACT FROM AUTHOR]

Published
2023
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35. Accuracy and applications of sequencing and genotyping approaches for CYP2A6 and homologous genes

Author

Langlois, Alec W R, El-Boraie, Ahmed, Fukunaga, Koya, Mushiroda, Taisei, Kubo, Michiaki, Lerman, Caryn, Knight, Jo, Scherer, Steven E, Chenoweth, Meghan J, Tyndale, Rachel F, Langlois, Alec W R, El-Boraie, Ahmed, Fukunaga, Koya, Mushiroda, Taisei, Kubo, Michiaki, Lerman, Caryn, Knight, Jo, Scherer, Steven E, Chenoweth, Meghan J, and Tyndale, Rachel F

Abstract

We evaluated multiple genotyping/sequencing approaches in a homologous region of chromosome 19, and investigated associations of two common 3'-UTR CYP2A6 variants with activity in vivo. Individuals (n = 1704) of European and African ancestry were phenotyped for the nicotine metabolite ratio (NMR), an index of CYP2A6 activity, and genotyped/sequenced using deep amplicon exon sequencing, SNP array, genotype imputation and targeted capture sequencing. Amplicon exon sequencing was the gold standard to which other methods were compared within-individual for CYP2A6, CYP2A7, CYP2A13, and CYP2B6 exons to identify highly discordant positions. Linear regression models evaluated the association of CYP2A6*1B and rs8192733 genotypes (coded additively) with logNMR. All approaches were ≤2.6% discordant with the gold standard; discordant calls were concentrated at few positions. Fifteen positions were discordant in >10% of individuals, with 12 appearing in regions of high identity between homologous genes (e.g. CYP2A6 and CYP2A7). For six, allele frequencies in our study and online databases were discrepant, suggesting errors in online sources. In the European-ancestry group (n = 935), CYP2A6*1B and rs8192733 were associated with logNMR (P <0.001). A combined model found main effects of both variants on increasing logNMR. Similar trends were found in those of African ancestry (n = 506). Multiple genotyping/sequencing approaches used in this chromosome 19 region contain genotyping/sequencing errors, as do online databases. Gene-specific primers and SNP array probes must consider gene homology; short-read sequencing of related genes in a single reaction should be avoided. Using improved sequencing approaches, we characterized two gain-of-function 3'-UTR variants, including the relatively understudied rs8192733. [Abstract copyright: Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.]

Published
2022

36. A genetic map of Xenopus tropicalis

Author

Wells, Dan E., Gutierrez, Laura, Xu, Zhenkang, Krylov, Vladimir, Macha, Jaroslav, Blankenburg, Kerstin P., Hitchens, Matthew, Bellot, Larry J., Spivey, Mary, Stemple, Derek L., Kowis, Andria, Ye, Yuan, Pasternak, Shiran, Owen, Jenetta, Tran, Thu, Slavikova, Renata, Tumova, Lucie, Tlapakova, Tereza, Seifertova, Eva, Scherer, Steven E., and Sater, Amy K.

Published
2011
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37. Forerunner Genes Contiguous to RB1 Contribute to the Development of in situ Neoplasia

Author

Lee, Sangkyou, Jeong, Joon, Majewski, Tadeusz, Scherer, Steven E., Kim, Mi-Sook, Tuziak, Tomasz, Tang, Kuang S., Baggerly, Keith, Grossman, Herbert Barton, Zhou, Jain-Hua, Shen, Lanlan, Bondaruk, Jolanta, Ahmed, Saira S., Samanta, Susmita, Spiess, Philippe, Wu, Xifeng, Filipek, Slawomir, McConkey, David, Bar-Eli, Menashe, Issa, Jean-Pierre, Benedict, William F., and Czerniak, Bogdan

Published
2007
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39. Variants in genes coding for collagen type IV α-chains are frequent causes of persistent, isolated hematuria during childhood.

Author

Alge, Joseph L., Bekheirnia, Nasim, Willcockson, Alexandra R., Qin, Xiang, Scherer, Steven E., Braun, Michael C., and Bekheirnia, Mir Reza

Subjects
KIDNEY physiology, KIDNEY disease diagnosis, COLLAGEN, DELAYED diagnosis, GENETIC mutation, SEQUENCE analysis, GENETIC testing, CLINICS, MEDICAL protocols, PATIENT monitoring, MEDICAL referrals, GENES, RESEARCH funding, HEMATURIA, URINALYSIS, LONGITUDINAL method, SECONDARY analysis, EARLY diagnosis, DISEASE risk factors, CHILDREN
Abstract

Background: Children with persistent, isolated microscopic hematuria typically undergo a limited diagnostic workup and are monitored for signs of kidney disease in long-term longitudinal follow-up, which can delay diagnosis and allow disease progression in some cases. Methods: To determine the clinical utility of genetic screening in this population, we performed targeted genetic testing using a custom, 32-gene next-generation sequencing panel for progressive kidney disease on children referred to the Texas Children's Hospital Pediatric Nephrology clinic for persistent, microscopic hematuria (n = 30; cohort 1). Patients with microscopic hematuria identified by urinalysis on at least two separate occasions were eligible for enrollment, but those with other evidence of kidney disease were excluded. Results were analyzed for sequence variants using the American College of Medical Genetics and Genomics (ACMG) guideline for data interpretation and were validated using a secondary analysis of a dataset of children with hematuria and normal kidney function who had undergone genetic testing as part of an industry-sponsored program (cohort 2; n = 67). Results: In cohort 1 33% of subjects (10/30) had pathogenic or likely pathogenic (P/LP) variants in the type IV collagen genes (COL4A3/A4/A5), and 10% (3/30) had variants of uncertain significance in these genes. The high diagnostic rate in type IV collagen genes was confirmed in cohort 2, where 27% (18/67) of subjects had P/LP variants in COL4A3/A4/A5 genes. Conclusions: Children with persistent, isolated microscopic hematuria have a high likelihood of having pathogenic variants in type IV collagen genes and genetic screening should be considered. [ABSTRACT FROM AUTHOR]

Published
2023
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41. Mutations in Smooth Muscle Alpha-Actin (ACTA2) Cause Coronary Artery Disease, Stroke, and Moyamoya Disease, Along with Thoracic Aortic Disease

Author

Guo, Dong-Chuan, Papke, Christina L., Tran-Fadulu, Van, Regalado, Ellen S., Avidan, Nili, Johnson, Ralph Jay, Kim, Dong H., Pannu, Hariyadarshi, Willing, Marcia C., Sparks, Elizabeth, Pyeritz, Reed E., Singh, Michael N., Dalman, Ronald L., Grotta, James C., Marian, Ali J., Boerwinkle, Eric A., Frazier, Lorraine Q., LeMaire, Scott A., Coselli, Joseph S., Estrera, Anthony L., Safi, Hazim J., Veeraraghavan, Sudha, Muzny, Donna M., Wheeler, David A., Willerson, James T., Yu, Robert K., Shete, Sanjay S., Scherer, Steven E., Raman, C.S., Buja, L. Maximilian, and Milewicz, Dianna M.

Published
2009
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42. Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy

Author

Majewski, Tadeusz, Lee, Sangkyou, Jeong, Joon, Yoon, Dong-Sup, Kram, Andrzej, Kim, Mi-Sook, Tuziak, Tomasz, Bondaruk, Jolanta, Lee, Sooyong, Park, Weon-Seo, Tang, Kuang S, Chung, Woonbok, Shen, Lanlan, Ahmed, Saira S, Johnston, Dennis A, Grossman, H Barton, Dinney, Colin P, Zhou, Jain-Hua, Harris, R Alan, Snyder, Carrie, Filipek, Slawomir, Narod, Steven A, Watson, Patrice, Lynch, Henry T, Gazdar, Adi, Bar-Eli, Menashe, Wu, Xifeng F, McConkey, David J, Baggerly, Keith, Issa, Jean-Pierre, Benedict, William F, Scherer, Steven E, and Czerniak, Bogdan

Published
2008
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43. Somatic mutations affect key pathways in lung adenocarcinoma

Author

Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, Sougnez, Carrie, Greulich, Heidi, Muzny, Donna M., Morgan, Margaret B., Fulton, Lucinda, Fulton, Robert S., Zhang, Qunyuan, Wendl, Michael C., Lawrence, Michael S., Larson, David E., Chen, Ken, Dooling, David J., Sabo, Aniko, Hawes, Alicia C., Shen, Hua, Jhangiani, Shalini N., Lewis, Lora R., Hall, Otis, Zhu, Yiming, Mathew, Tittu, Ren, Yanru, Yao, Jiqiang, Scherer, Steven E., Clerc, Kerstin, Metcalf, Ginger A., Ng, Brian, Milosavljevic, Aleksandar, Gonzalez-Garay, Manuel L., Osborne, John R., Meyer, Rick, Shi, Xiaoqi, Tang, Yuzhu, Koboldt, Daniel C., Lin, Ling, Abbott, Rachel, Miner, Tracie L., Pohl, Craig, Fewell, Ginger, Haipek, Carrie, Schmidt, Heather, Dunford-Shore, Brian H., Kraja, Aldi, Crosby, Seth D., Sawyer, Christopher S., Vickery, Tammi, Sander, Sacha, Robinson, Jody, Winckler, Wendy, Baldwin, Jennifer, Chirieac, Lucian R., Dutt, Amit, Fennell, Tim, Hanna, Megan, Johnson, Bruce E., Onofrio, Robert C., Thomas, Roman K., Tonon, Giovanni, Weir, Barbara A., Zhao, Xiaojun, Ziaugra, Liuda, Zody, Michael C., Giordano, Thomas, Orringer, Mark B., Roth, Jack A., Spitz, Margaret R., Wistuba, Ignacio I., Ozenberger, Bradley, Good, Peter J., Chang, Andrew C., Beer, David G., Watson, Mark A., Ladanyi, Marc, Broderick, Stephen, Yoshizawa, Akihiko, Travis, William D., Pao, William, Province, Michael A., Weinstock, George M., Varmus, Harold E., Gabriel, Stacey B., Lander, Eric S., Gibbs, Richard A., Meyerson, Matthew, and Wilson, Richard K.

Subjects
Diagnosis, Care and treatment, Physiological aspects, Genetic aspects, Research, Prognosis, Lung cancer -- Genetic aspects -- Research -- Care and treatment -- Diagnosis -- Prognosis, Adenocarcinoma -- Genetic aspects -- Research -- Care and treatment -- Prognosis -- Diagnosis, Gene mutation -- Research -- Physiological aspects -- Genetic aspects, DNA sequencing -- Research -- Physiological aspects -- Genetic aspects, Gene mutations -- Research -- Physiological aspects -- Genetic aspects, Nucleotide sequencing -- Research -- Physiological aspects -- Genetic aspects
Abstract

Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations [...]

Published
2008

44. The finished DNA sequence of human chromosome 12

Author

Scherer, Steven E., Muzny, Donna M., Buhay, Christian J., Chen, Rui, Cree, Andrew, Ding, Yan, Dugan-Rocha, Shannon, Gill, Rachel, Gunaratne, Preethi, Harris, R. Alan, Hawes, Alicia C., Hernandez, Judith, Hodgson, Anne V., Hume, Jennifer, Jackson, Andrew, Khan, Ziad Mohid, Kovar-Smith, Christie, Lewis, Lora R., Lozado, Ryan J., Metzker, Michael L., Milosavljevic, Aleksandar, Miner, George R., Montgomery, Kate T., Morgan, Margaret B., Nazareth, Lynne V., Scott, Graham, Sodergren, Erica, Song, Xing-Zhi, Steffen, David, Lovering, Ruth C., Wheeler, David A., Worley, Kim C., Yuan, Yi, Zhang, Zhengdong, Adams, Charles Q., Ansari-Lari, M. Ali, Ayele, Mulu, Brown, Mary J., Chen, Guan, Chen, Zhijian, Clerc-Blankenburg, Kerstin P., Davis, Clay, Delgado, Oliver, Dinh, Huyen H., Draper, Heather, Gonzalez-Garay, Manuel L., Havlak, Paul, Jackson, Laronda R., Jacob, Leni S., Kelly, Susan H., Li, Li, Li, Zhangwan, Liu, Jing, Liu, Wen, Lu, Jing, Maheshwari, Manjula, Nguyen, Bao-Viet, Okwuonu, Geoffrey O., Pasternak, Shiran, Perez, Lesette M., Plopper, Farah J. H., Santibanez, Jireh, Shen, Hua, Tabor, Paul E., Verduzco, Daniel, Waldron, Lenee, Wang, Qiaoyan, Williams, Gabrielle A., Zhang, JingKun, Zhou, Jianling, Nelson, David, Kucherlapati, Raju, Weinstock, George, and Gibbs, Richard A.

Published
2006
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45. The DNA sequence, annotation and analysis of human chromosome 3

Author

Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, Sudbrak, Ralf, Buhay, Christian J., Chen, Rui, Cree, Andrew, Ding, Yan, Dugan-Rocha, Shannon, Gill, Rachel, Gunaratne, Preethi, Harris, R. Alan, Hawes, Alicia C., Hernandez, Judith, Hodgson, Anne V., Hume, Jennifer, Jackson, Andrew, Khan, Ziad Mohid, Kovar-Smith, Christie, Lewis, Lora R., Lozado, Ryan J., Metzker, Michael L., Milosavljevic, Aleksandar, Miner, George R., Morgan, Margaret B., Nazareth, Lynne V., Scott, Graham, Sodergren, Erica, Song, Xing-Zhi, Steffen, David, Wei, Sharon, Wheeler, David A., Wright, Mathew W., Worley, Kim C., Yuan, Ye, Zhang, Zhengdong, Adams, Charles Q., Ansari-Lari, M. Ali, Ayele, Mulu, Brown, Mary J., Chen, Guan, Chen, Zhijian, Clendenning, James, Clerc-Blankenburg, Kerstin P., Chen, Runsheng, Chen, Zhu, Davis, Clay, Delgado, Oliver, Dinh, Huyen H., Dong, Wei, Draper, Heather, Ernst, Stephen, Fu, Gang, Gonzalez-Garay, Manuel L., Garcia, Dawn K., Gillett, Will, Gu, Jun, Hao, Bailin, Haugen, Eric, Havlak, Paul, He, Xin, Hennig, Steffen, Hu, Songnian, Huang, Wei, Jackson, Laronda R., Jacob, Leni S., Kelly, Susan H., Kube, Michael, Levy, Ruth, Li, Zhangwan, Liu, Bin, Liu, Jing, Liu, Wen, Lu, Jing, Maheshwari, Manjula, Nguyen, Bao-Viet, Okwuonu, Geoffrey O., Palmeiri, Anthony, Pasternak, Shiran, Perez, Lesette M., Phelps, Karen A., Plopper, Farah J. H., Qiang, Boqin, Raymond, Christopher, Rodriguez, Ruben, Saenphimmachak, Channakhone, Santibanez, Jireh, Shen, Hua, Shen, Yan, Subramanian, Sandhya, Tabor, Paul E., Verduzco, Daniel, Waldron, Lenee, Wang, Jian, Wang, Jun, Wang, Qiaoyan, Williams, Gabrielle A., Wong, Gane K.-S., Yao, Zhijian, Zhang, JingKun, Zhang, Xiuqing, Zhao, Guoping, Zhou, Jianling, Zhou, Yang, contributors, further, Nelson, David, Lehrach, Hans, Reinhardt, Richard, Naylor, Susan L., Yang, Huanming, Olson, Maynard, Weinstock, George, and Gibbs, Richard A.

Abstract

Author(s): Donna M. Muzny [1]; Steven E. Scherer (corresponding author) [1]; Rajinder Kaul [2]; Jing Wang [3]; Jun Yu [3]; Ralf Sudbrak [4, 5]; Christian J. Buhay [1]; Rui Chen [...]

Published
2006
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46. Recurring germline mosaicism in a family due to reversion of an inherited derivative chromosome 8 from an 8;21 translocation with interstitial telomeric sequences

Author

Bi, Weimin, Yuan, Bo, Liu, Pengfei, Murry, Jaclyn B, Qin, Xiang, Xia, Fan, Quach, Thao, Cooper, Lance M, Wiszniewska, Joanna, Hixson, Patricia, Peacock, Sandra, Tonk, Vijay S, Huff, Robert W, Ortega, Veronica, Lupski, James R, Scherer, Steven E, Littlejohn, Rebecca Okashah, Velagaleti, Gopalrao V N, Roeder, Elizabeth R, and Cheung, Sau Wai

Abstract

BackgroundMosaicism for chromosomal structural abnormalities, other than marker or ring chromosomes, is rarely inherited.MethodsWe performed cytogenetics studies and breakpoint analyses on a family with transmission of mosaicism for a derivative chromosome 8 (der(8)), resulting from an unbalanced translocation between the long arms of chromosomes 8 and 21 over three generations.ResultsThe proband and his maternal half-sister had mosaicism for a der(8) cell line leading to trisomy of the distal 21q, and both had Down syndrome phenotypic features. Mosaicism for a cell line with the der(8) and a normal cell line was also detected in a maternal half-cousin. The der(8) was inherited from the maternal grandmother who had four abnormal cell lines containing the der(8), in addition to a normal cell line. One maternal half-aunt had the der(8) and an isodicentric chromosome 21 (idic(21)). Sequencing studies revealed microhomologies at the junctures of the der(8) and idic(21) in the half-aunt, suggesting a replicative mechanism in the rearrangement formation. Furthermore, interstitial telomeric sequences (ITS) were identified in the juncture between chromosomes 8 and 21 in the der(8).ConclusionMosaicism in the proband, his half-sister and half-cousin resulting from loss of chromosome 21 material from the der(8) appears to be a postzygotic event due to the genomic instability of ITS and associated with selective growth advantage of normal cells. The reversion of the inherited der(8) to a normal chromosome 8 in this family resembles revertant mosaicism of point mutations. We propose that ITS could mediate recurring revertant mosaicism for some constitutional chromosomal structural abnormalities.

Published
2023
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49. Initial sequencing and analysis of the human genome

Author

Lander, Eric S., Linton, Lauren M., Birren, Bruce, Nusbaum, Chad, Zody, Michael C., Baldwin, Jennifer, Devon, Keri, Dewar, Ken, Doyle, Michael, FitzHugh, William, Funke, Roel, Gage, Diane, Harris, Katrina, Heaford, Andrew, Howland, John, Kann, Lisa, Lehoczky, Jessica, LeVine, Rosie, McEwan, Paul, McKernan, Kevin, Meldrim, James, Mesirov, Jill P., Miranda, Cher, Morris, William, Naylor, Jerome, Raymond, Christina, Rosetti, Mark, Santos, Ralph, Sheridan, Andrew, Sougnez, Carrie, Stange-Thomann, Nicole, Stojanovic, Nikola, Subramanian, Aravind, Wyman, Dudley, Rogers, Jane, Sulston, John, Ainscough, Rachael, Beck, Stephan, Bentley, David, Burton, John, Clee, Christopher, Carter, Nigel, Coulson, Alan, Deadman, Rebecca, Deloukas, Panos, Dunham, Andrew, Dunham, Ian, Durbin, Richard, French, Lisa, Grafham, Darren, Gregory, Simon, Hubbard, Tim, Humphray, Sean, Hunt, Adrienne, Jones, Matthew, Lloyd, Christine, McMurray, Amanda, Matthews, Lucy, Mercer, Simon, Milne, Sarah, Mullikin, James C., Mungall, Andrew, Plumb, Robert, Ross, Mark, Shownkeen, Ratna, Sims, Sarah, Waterston, Robert H., Wilson, Richard K., Hillier, LaDeana W., McPherson, John D., Marra, Marco A., Mardis, Elaine R., Fulton, Lucinda A., Chinwalla, Asif T., Pepin, Kymberlie H., Gish, Warren R., Chissoe, Stephanie L., Wendl, Michael C., Delehaunty, Kim D., Miner, Tracie L., Delehaunty, Andrew, Kramer, Jason B., Cook, Lisa L., Fulton, Robert S., Johnson, Douglas L., Minx, Patrick J., Clifton, Sandra W., Hawkins, Trevor, Branscomb, Elbert, Predki, Paul, Richardson, Paul, Wenning, Sarah, Slezak, Tom, Doggett, Norman, Cheng, Jan-Fang, Olsen, Anne, Lucas, Susan, Elkin, Christopher, Uberbacher, Edward, Frazier, Marvin, Gibbs, Richard A., Muzny, Donna M., Scherer, Steven E., Bouck, John B., Sodergren, Erica J., Worley, Kim C., Rives, Catherine M., Gorrell, James H., Metzker, Michael L., Naylor, Susan L., Kucherlapati, Raju S., Nelson, David L., Weinstock, George M., Sakaki, Yoshiyuki, Fujiyama, Asao, Hattori, Masahira, Yada, Tetsushi, Toyoda, Atsushi, Itoh, Takehiko, Kawagoe, Chiharu, Watanabe, Hidemi, Totoki, Yasushi, Taylor, Todd, Weissenbach, Jean, Heilig, Roland, Saurin, William, Artiguenave, Francois, Brottier, Philippe, Bruls, Thomas, Pelletier, Eric, Robert, Catherine, Wincker, Patrick, Rosenthal, Andre, Platzer, Matthias, Nyakatura, Gerald, Taudien, Stefan, Rump, Andreas, Smith, Douglas R., Doucette-Stamm, Lynn, Rubenfield, Marc, Weinstock, Keith, Lee, Hong Mei, Dubois, JoAnn, Yang, Huanming, Yu, Jun, Wang, Jian, Huang, Guyang, Gu, Jun, Hood, Leroy, Rowen, Lee, Madan, Anup, Qin, Shizen, Davis, Ronald W., Federspiel, Nancy A., Abola, A. Pia, Proctor, Michael J., Roe, Bruce A., Chen, Feng, Pan, Huaqin, Ramser, Juliane, Lehrach, Hans, Reinhardt, Richard, McCombie, W. Richard, de la Bastide, Melissa, Dedhia, Neilay, Blocker, Helmut, Hornischer, Klaus, Nordsiek, Gabriele, Agarwala, Richa, Aravind, L., Bailey, Jeffrey A., Bateman, Alex, Batzoglou, Serafim, Birney, Ewan, Bork, Peer, Brown, Daniel G., Burge, Christopher B., Cerutti, Lorenzo, Chen, Hsiu-Chuan, Church, Deanna, Clamp, Michele, Copley, Richard R., Doerks, Tobias, Eddy, Sean R., Eichler, Evan E., Furey, Terrence S., Galagan, James, Gilbert, James G. R., Harmon, Cyrus, Hayashizaki, Yoshihide, Haussler, David, Hermjakob, Henning, Hokamp, Karsten, Jang, Wonhee, Johnson, L. Steven, Jones, Thomas A., Kasif, Simon, Kaspryzk, Arek, Kennedy, Scot, Kent, W. James, Kitts, Paul, Koonin, Eugene V., Korf, Ian, Kulp, David, Lancet, Doron, Lowe, Todd M., McLysaght, Aoife, Mikkelsen, Tarjei, Moran, John V., Mulder, Nicola, Pollara, Victor J., Ponting, Chris P., Schuler, Greg, Schultz, Jorg, Slater, Guy, Smit, Arian F. A., Stupka, Elia, Szustakowki, Joseph, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Wagner, Lukas, Wallis, John, Wheeler, Raymond, Williams, Alan, Wolf, Yuri I., Wolfe, Kenneth H., Yang, Shiaw-Pyng, Yeh, Ru-Fang, Collins, Francis, Guyer, Mark S., Peterson, Jane, Felsenfeld, Adam, Wetterstrand, Kris A., Myers, Richard M., Schmutz, Jeremy, Dickson, Mark, Grimwood, Jane, Cox, David R., Olson, Maynard V., Kaul, Rajinder, Raymond, Christopher, Shimizu, Nobuyoshi, Kawasaki, Kazuhiko, Minoshima, Shinsei, Evans, Glen A., Athanasiou, Maria, Schultz, Roger, Patrinos, Aristides, and Morgan, Michael J.

Abstract

Author(s): International Human Genome Sequencing Consortium; Whitehead Institute for Biomedical Research, Center for Genome Research:; Eric S. Lander [1]; Lauren M. Linton [1]; Bruce Birren [1]; Chad Nusbaum [1]; Michael [...]

Published
2001
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