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1. Single-cell T-cell receptor repertoire profiling in dogs

Author

Hoang, My H., Skidmore, Zachary L., Rindt, Hans, Chu, Shirley, Fisk, Bryan, Foltz, Jennifer A., Fronick, Catrina, Fulton, Robert, Zhou, Mingyi, Bivens, Nathan J., Reinero, Carol N., Fehniger, Todd A., Griffith, Malachi, Bryan, Jeffrey N., and Griffith, Obi L.

Published
2024
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2. A draft human pangenome reference

Author

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

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

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

Published
2023

3. Gaps and complex structurally variant loci in phased genome assemblies

Author

Porubsky, David, Vollger, Mitchell R, Harvey, William T, Rozanski, Allison N, Ebert, Peter, Hickey, Glenn, Hasenfeld, Patrick, Sanders, Ashley D, Stober, Catherine, Consortium, Human Pangenome Reference, Korbel, Jan O, Paten, Benedict, Marschall, Tobias, Eichler, Evan E, Abel, Haley J, Antonacci-Fulton, Lucinda L, Asri, Mobin, Baid, Gunjan, Baker, Carl A, Belyaeva, Anastasiya, Billis, Konstantinos, Bourque, Guillaume, Buonaiuto, Silvia, Carroll, Andrew, Chaisson, Mark JP, Chang, Pi-Chuan, Chang, Xian H, Cheng, Haoyu, Chu, Justin, Cody, Sarah, Colonna, Vincenza, Cook, Daniel E, Cook-Deegan, Robert M, Cornejo, Omar E, Diekhans, Mark, Doerr, Daniel, Ebler, Jana, Eizenga, Jordan M, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L, Feng, Xiaowen, Fischer, Christian, Flicek, Paul, Formenti, Giulio, Frankish, Adam, Fulton, Robert S, Gao, Yan, Garg, Shilpa, Garrison, Erik, Garrison, Nanibaa’ A, Giron, Carlos Garcia, Green, Richard E, Groza, Cristian, Guarracino, Andrea, Haggerty, Leanne, Hall, Ira M, Haukness, Marina, Haussler, David, Heumos, Simon, Hoekzema, Kendra, Hourlier, Thibaut, Howe, Kerstin, Jain, Miten, Jarvis, Erich D, Ji, Hanlee P, Kenny, Eimear E, Koenig, Barbara A, Kolesnikov, Alexey, Kordosky, Jennifer, Koren, Sergey, Lee, HoJoon, Lewis, Alexandra P, Li, Heng, Liao, Wen-Wei, Lu, Shuangjia, Lu, Tsung-Yu, Lucas, Julian K, Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, Markello, Charles, Martin, Fergal J, McCartney, Ann, McDaniel, Jennifer, Miga, Karen H, Mitchell, Matthew W, Monlong, Jean, Mountcastle, Jacquelyn, Munson, Katherine M, Mwaniki, Moses Njagi, Nattestad, Maria, Novak, Adam M, and Nurk, Sergey

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Humans, DNA, Satellite, Polymorphism, Genetic, Haplotypes, Segmental Duplications, Genomic, Sequence Analysis, DNA, Human Pangenome Reference Consortium, Medical and Health Sciences, Bioinformatics
Abstract

There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6-7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation.

Published
2023

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

Author

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

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

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

Published
2022

5. Neoantigen landscape supports feasibility of personalized cancer vaccine for follicular lymphoma

Author

Ramirez, Cody A., Becker-Hapak, Michelle, Singhal, Kartik, Russler-Germain, David A., Frenkel, Felix, Barnell, Erica K., McClain, Ethan D., Desai, Sweta, Schappe, Timothy, Onyeador, Onyinyechi C., Kudryashova, Olga, Belousov, Vladislav, Bagaev, Alexander, Ocheredko, Elena, Kiwala, Susanna, Hundal, Jasreet, Skidmore, Zachary L., Watkins, Marcus P., Mooney, Thomas B., Walker, Jason R., Krysiak, Kilannin, Gomez, Felicia, Fronick, Catrina C., Fulton, Robert S., Schreiber, Robert D., Mehta-Shah, Neha, Cashen, Amanda F., Kahl, Brad S., Ataullakhanov, Ravshan, Bartlett, Nancy L., Griffith, Malachi, Griffith, Obi L., and Fehniger, Todd A.

Published
2024
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6. The Human Pangenome Project: a global resource to map genomic diversity

Author

Wang, Ting, Antonacci-Fulton, Lucinda, Howe, Kerstin, Lawson, Heather A, Lucas, Julian K, Phillippy, Adam M, Popejoy, Alice B, Asri, Mobin, Carson, Caryn, Chaisson, Mark JP, Chang, Xian, Cook-Deegan, Robert, Felsenfeld, Adam L, Fulton, Robert S, Garrison, Erik P, Garrison, Nanibaa’ A, Graves-Lindsay, Tina A, Ji, Hanlee, Kenny, Eimear E, Koenig, Barbara A, Li, Daofeng, Marschall, Tobias, McMichael, Joshua F, Novak, Adam M, Purushotham, Deepak, Schneider, Valerie A, Schultz, Baergen I, Smith, Michael W, Sofia, Heidi J, Weissman, Tsachy, Flicek, Paul, Li, Heng, Miga, Karen H, Paten, Benedict, Jarvis, Erich D, Hall, Ira M, Eichler, Evan E, and Haussler, David

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Genome, Human, Genomics, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, DNA, Human Pangenome Reference Consortium, General Science & Technology
Abstract

The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation. A high-quality reference with global representation of common variants, including single-nucleotide variants, structural variants and functional elements, is needed. The Human Pangenome Reference Consortium aims to create a more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity. Here we leverage innovations in technology, study design and global partnerships with the goal of constructing the highest-possible quality human pangenome reference. Our goal is to improve data representation and streamline analyses to enable routine assembly of complete diploid genomes. With attention to ethical frameworks, the human pangenome reference will contain a more accurate and diverse representation of global genomic variation, improve gene-disease association studies across populations, expand the scope of genomics research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine.

Published
2022

7. The complete sequence of a human genome

Author

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

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

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

Published
2022

8. A domestic cat whole exome sequencing resource for trait discovery.

Author

Rodney, Alana R, Buckley, Reuben M, Fulton, Robert S, Fronick, Catrina, Richmond, Todd, Helps, Christopher R, Pantke, Peter, Trent, Dianne J, Vernau, Karen M, Munday, John S, Lewin, Andrew C, Middleton, Rondo, Lyons, Leslie A, and Warren, Wesley C

Abstract

Over 94 million domestic cats are susceptible to cancers and other common and rare diseases. Whole exome sequencing (WES) is a proven strategy to study these disease-causing variants. Presented is a 35.7 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. Whole exome sequencing was conducted on 41 cats with known and unknown genetic diseases and traits, of which ten cats had matching whole genome sequence (WGS) data available, used to validate WES performance. At 80 × mean exome depth of coverage, 96.4% of on-target base coverage had a sequencing depth > 20-fold, while over 98% of single nucleotide variants (SNVs) identified by WGS were also identified by WES. Platform-specific SNVs were restricted to sex chromosomes and a small number of olfactory receptor genes. Within the 41 cats, we identified 31 previously known causal variants and discovered new gene candidate variants, including novel missense variance for polycystic kidney disease and atrichia in the Peterbald cat. These results show the utility of WES to identify novel gene candidate alleles for diseases and traits for the first time in a feline model.

Published
2021

9. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author

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

Published
2023
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10. Genomic landscape of TP53-mutated myeloid malignancies

Author

Abel, Haley J., Oetjen, Karolyn A., Miller, Christopher A., Ramakrishnan, Sai M., Day, Ryan B., Helton, Nichole M., Fronick, Catrina C., Fulton, Robert S., Heath, Sharon E., Tarnawsky, Stefan P., Nonavinkere Srivatsan, Sridhar, Duncavage, Eric J., Schroeder, Molly C., Payton, Jacqueline E., Spencer, David H., Walter, Matthew J., Westervelt, Peter, DiPersio, John F., Ley, Timothy J., and Link, Daniel C.

Published
2023
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11. Utility of targeted gene sequencing to differentiate myeloid malignancies from other cytopenic conditions

Author

DeZern, Amy E., Goll, Johannes B., Lindsley, R. Coleman, Bejar, Rafael, Wilson, Steffanie H., Hebert, Donnie, Deeg, Joachim, Zhang, Ling, Gore, Steven, Al Baghdadi, Tareq, Maciejewski, Jaroslaw, Liu, Jane, Padron, Eric, Komrojki, Rami, Saber, Wael, Abel, Gregory, Kroft, Steven H., Harrington, Alexandra, Grimes, Tyler, Reed, Harrison, Fulton, Robert S., DiFronzo, Nancy L., Gillis, Nancy, Sekeres, Mikkael A., and Walter, Matthew J.

Published
2023
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12. Telomere-to-telomere assembly of a complete human X chromosome

Author

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

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

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

Published
2020

13. Immunosuppression and outcomes in adult patients with de novo acute myeloid leukemia with normal karyotypes

Author

Ferraro, Francesca, Miller, Christopher A., Christensen, Keegan A., Helton, Nichole M., O’Laughlin, Margaret, Fronick, Catrina C., Fulton, Robert S., Kohlschmidt, Jessica, Eisfeld, Ann-Kathrin, Bloomfield, Clara D., Ramakrishnan, Sai Mukund, Day, Ryan B., Wartman, Lukas D., Uy, Geoffrey L., Welch, John S., Christopher, Matthew J., Heath, Sharon E., Baty, Jack D., Schuelke, Matthew J., Payton, Jacqueline E., Spencer, David H., Rettig, Michael P., Link, Daniel C., Walter, Matthew J., Westervelt, Peter, DiPersio, John F., and Ley, Timothy J.

Published
2021

14. Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer

Author

Cui Zhou, Daniel, Jayasinghe, Reyka G., Chen, Siqi, Herndon, John M., Iglesia, Michael D., Navale, Pooja, Wendl, Michael C., Caravan, Wagma, Sato, Kazuhito, Storrs, Erik, Mo, Chia-Kuei, Liu, Jingxian, Southard-Smith, Austin N., Wu, Yige, Naser Al Deen, Nataly, Baer, John M., Fulton, Robert S., Wyczalkowski, Matthew A., Liu, Ruiyang, Fronick, Catrina C., Fulton, Lucinda A., Shinkle, Andrew, Thammavong, Lisa, Zhu, Houxiang, Sun, Hua, Wang, Liang-Bo, Li, Yize, Zuo, Chong, McMichael, Joshua F., Davies, Sherri R., Appelbaum, Elizabeth L., Robbins, Keenan J., Chasnoff, Sara E., Yang, Xiaolu, Reeb, Ashley N., Oh, Clara, Serasanambati, Mamatha, Lal, Preet, Varghese, Rajees, Mashl, Jay R., Ponce, Jennifer, Terekhanova, Nadezhda V., Yao, Lijun, Wang, Fang, Chen, Lijun, Schnaubelt, Michael, Lu, Rita Jui-Hsien, Schwarz, Julie K., Puram, Sidharth V., Kim, Albert H., Song, Sheng-Kwei, Shoghi, Kooresh I., Lau, Ken S., Ju, Tao, Chen, Ken, Chatterjee, Deyali, Hawkins, William G., Zhang, Hui, Achilefu, Samuel, Chheda, Milan G., Oh, Stephen T., Gillanders, William E., Chen, Feng, DeNardo, David G., Fields, Ryan C., and Ding, Li

Published
2022
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15. Exome sequencing of Finnish isolates enhances rare-variant association power

Author

Locke, Adam E, Steinberg, Karyn Meltz, Chiang, Charleston WK, Service, Susan K, Havulinna, Aki S, Stell, Laurel, Pirinen, Matti, Abel, Haley J, Chiang, Colby C, Fulton, Robert S, Jackson, Anne U, Kang, Chul Joo, Kanchi, Krishna L, Koboldt, Daniel C, Larson, David E, Nelson, Joanne, Nicholas, Thomas J, Pietilä, Arto, Ramensky, Vasily, Ray, Debashree, Scott, Laura J, Stringham, Heather M, Vangipurapu, Jagadish, Welch, Ryan, Yajnik, Pranav, Yin, Xianyong, Eriksson, Johan G, Ala-Korpela, Mika, Järvelin, Marjo-Riitta, Männikkö, Minna, Laivuori, Hannele, Dutcher, Susan K, Stitziel, Nathan O, Wilson, Richard K, Hall, Ira M, Sabatti, Chiara, Palotie, Aarno, Salomaa, Veikko, Laakso, Markku, Ripatti, Samuli, Boehnke, Michael, and Freimer, Nelson B

Subjects
Medical Biochemistry and Metabolomics, Biological Sciences, Biomedical and Clinical Sciences, Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Alleles, Cholesterol, HDL, Cluster Analysis, Endpoint Determination, Finland, Genetic Association Studies, Genetic Predisposition to Disease, Genetic Variation, Geographic Mapping, Humans, Multifactorial Inheritance, Quantitative Trait Loci, Reproducibility of Results, Exome Sequencing, FinnGen Project, General Science & Technology
Abstract

Exome-sequencing studies have generally been underpowered to identify deleterious alleles with a large effect on complex traits as such alleles are mostly rare. Because the population of northern and eastern Finland has expanded considerably and in isolation following a series of bottlenecks, individuals of these populations have numerous deleterious alleles at a relatively high frequency. Here, using exome sequencing of nearly 20,000 individuals from these regions, we investigate the role of rare coding variants in clinically relevant quantitative cardiometabolic traits. Exome-wide association studies for 64 quantitative traits identified 26 newly associated deleterious alleles. Of these 26 alleles, 19 are either unique to or more than 20 times more frequent in Finnish individuals than in other Europeans and show geographical clustering comparable to Mendelian disease mutations that are characteristic of the Finnish population. We estimate that sequencing studies of populations without this unique history would require hundreds of thousands to millions of participants to achieve comparable association power.

Published
2019

22. High-resolution comparative analysis of great ape genomes

Author

Kronenberg, Zev N, Fiddes, Ian T, Gordon, David, Murali, Shwetha, Cantsilieris, Stuart, Meyerson, Olivia S, Underwood, Jason G, Nelson, Bradley J, Chaisson, Mark JP, Dougherty, Max L, Munson, Katherine M, Hastie, Alex R, Diekhans, Mark, Hormozdiari, Fereydoun, Lorusso, Nicola, Hoekzema, Kendra, Qiu, Ruolan, Clark, Karen, Raja, Archana, Welch, AnneMarie E, Sorensen, Melanie, Baker, Carl, Fulton, Robert S, Armstrong, Joel, Graves-Lindsay, Tina A, Denli, Ahmet M, Hoppe, Emma R, Hsieh, PingHsun, Hill, Christopher M, Pang, Andy Wing Chun, Lee, Joyce, Lam, Ernest T, Dutcher, Susan K, Gage, Fred H, Warren, Wesley C, Shendure, Jay, Haussler, David, Schneider, Valerie A, Cao, Han, Ventura, Mario, Wilson, Richard K, Paten, Benedict, Pollen, Alex, and Eichler, Evan E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Stem Cell Research, Human Genome, Biotechnology, Aetiology, Underpinning research, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Generic health relevance, Animals, Contig Mapping, Evolution, Molecular, Genetic Variation, Genome, Human, Hominidae, Humans, Molecular Sequence Annotation, Sequence Analysis, DNA, General Science & Technology
Abstract

Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.

Published
2018

23. The Integrated Genomic Landscape of Thymic Epithelial Tumors

Author

Radovich, Milan, Pickering, Curtis R, Felau, Ina, Ha, Gavin, Zhang, Hailei, Jo, Heejoon, Hoadley, Katherine A, Anur, Pavana, Zhang, Jiexin, McLellan, Mike, Bowlby, Reanne, Matthew, Thomas, Danilova, Ludmila, Hegde, Apurva M, Kim, Jaegil, Leiserson, Mark DM, Sethi, Geetika, Lu, Charles, Ryan, Michael, Su, Xiaoping, Cherniack, Andrew D, Robertson, Gordon, Akbani, Rehan, Spellman, Paul, Weinstein, John N, Hayes, D Neil, Raphael, Ben, Lichtenberg, Tara, Leraas, Kristen, Zenklusen, Jean Claude, Network, The Cancer Genome Atlas, Ally, Adrian, Appelbaum, Elizabeth L, Auman, J Todd, Balasundaram, Miruna, Balu, Saianand, Behera, Madhusmita, Beroukhim, Rameen, Berrios, Mario, Blandino, Giovanni, Bodenheimer, Tom, Bootwalla, Moiz S, Bowen, Jay, Brooks, Denise, Carcano, Flavio M, Carlsen, Rebecca, Carvalho, Andre L, Castro, Patricia, Chalabreysse, Lara, Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cope, Leslie, Cordes, Matthew G, Crain, Daniel, Curley, Erin, Defreitas, Timothy, Demchok, John A, Detterbeck, Frank, Dhalla, Noreen, Dienemann, Hendrik, Edenfield, W Jeff, Facciolo, Francesco, Ferguson, Martin L, Frazer, Scott, Fronick, Catrina C, Fulton, Lucinda A, Fulton, Robert S, Gabriel, Stacey B, Gardner, Johanna, Gastier-Foster, Julie M, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Heiman, David I, Hobensack, Shital, Holbrook, Andrea, Holt, Robert A, Hoyle, Alan P, Hutter, Carolyn M, Ittmann, Michael, Jefferys, Stuart R, Jones, Corbin D, Jones, Steven JM, Kasaian, Katayoon, Kimes, Patrick K, Lai, Phillip H, Laird, Peter W, Lawrence, Michael S, Lin, Pei, Liu, Jia, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T, and Mallery, David

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Autoimmune Disease, Biotechnology, Human Genome, Cancer, Rare Diseases, 2.1 Biological and endogenous factors, Aetiology, Adolescent, Adult, Aged, Aged, 80 and over, Female, Genomics, Humans, Male, Middle Aged, Mutation, Neoplasms, Glandular and Epithelial, Thymoma, Thymus Neoplasms, Transcription Factors, TFII, Young Adult, Cancer Genome Atlas Network, TCGA, autoimmunity, genomics, myasthenia gravis, proteomics, thymic carcinoma, thymic epithelial tumors, thymoma, transcriptomics, Neurosciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis. We further observe enrichment of mutations in HRAS, NRAS, and TP53. Last, we identify a molecular link between thymoma and the autoimmune disease myasthenia gravis, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy.

Published
2018

24. Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Author

Network, The Cancer Genome Atlas Research, Abeshouse, Adam, Adebamowo, Clement, Adebamowo, Sally N, Akbani, Rehan, Akeredolu, Teniola, Ally, Adrian, Anderson, Matthew L, Anur, Pavana, Appelbaum, Elizabeth L, Armenia, Joshua, Auman, J Todd, Bailey, Matthew H, Baker, Laurence, Balasundaram, Miruna, Balu, Saianand, Barthel, Floris P, Bartlett, John, Baylin, Stephen B, Behera, Madhusmita, Belyaev, Dmitry, Bennett, Joesph, Benz, Christopher, Beroukhim, Rameen, Birrer, Michael, Bocklage, Thèrése, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S, Bowen, Jay, Bowlby, Reanne, Boyd, Jeff, Brohl, Andrew S, Brooks, Denise, Byers, Lauren, Carlsen, Rebecca, Castro, Patricia, Chen, Hsiao-Wei, Cherniack, Andrew D, Chibon, Fréderic, Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cooper, Lee AD, Cope, Leslie, Cordes, Matthew G, Crain, Daniel, Curley, Erin, Danilova, Ludmila, Dao, Fanny, Davis, Ian J, Davis, Lara E, Defreitas, Timothy, Delman, Keith, Demchok, John A, Demetri, George D, Demicco, Elizabeth G, Dhalla, Noreen, Diao, Lixia, Ding, Li, DiSaia, Phil, Dottino, Peter, Doyle, Leona A, Drill, Esther, Dubina, Michael, Eschbacher, Jennifer, Fedosenko, Konstantin, Felau, Ina, Ferguson, Martin L, Frazer, Scott, Fronick, Catrina C, Fulidou, Victoria, Fulton, Lucinda A, Fulton, Robert S, Gabriel, Stacey B, Gao, Jianjiong, Gao, Qingsong, Gardner, Johanna, Gastier-Foster, Julie M, Gay, Carl M, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Godwin, Andrew K, Godwin, Eryn M, Gordienko, Elena, Grilley-Olson, Juneko E, Gutman, David A, Gutmann, David H, Hayes, D Neil, Hegde, Apurva M, Heiman, David I, Heins, Zachary, Helsel, Carmen, Hepperla, Austin J, Higgins, Kelly, Hoadley, Katherine A, and Hobensack, Shital

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Cancer, Human Genome, Digestive Diseases, Rare Diseases, Adult, Aged, Aged, 80 and over, Cluster Analysis, DNA Copy Number Variations, Epigenomics, Genome, Human, Genome-Wide Association Study, Humans, Middle Aged, Mutation, Sarcoma, Young Adult, Cancer Genome Atlas Research Network. Electronic address: elizabeth.demicco@sinaihealthsystem.ca, Cancer Genome Atlas Research Network, DNA methylation, The Cancer Genome Atlas, dedifferentiated liposarcoma, genomics, immune infiltration, leiomyosarcoma, molecular subtype, myxofibrosarcoma, pleomorphism, undifferentiated pleomorphic sarcoma, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (TP53, ATRX, RB1) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types.

Published
2017

26. Remethylation of Dnmt3a −/− hematopoietic cells is associated with partial correction of gene dysregulation and reduced myeloid skewing

Author

Ketkar, Shamika, Verdoni, Angela M., Smith, Amanda M., Bangert, Celia V., Leight, Elizabeth R., Chen, David Y., Brune, Meryl K., Helton, Nichole M., Hoock, Mieke, George, Daniel R., Fronick, Catrina, Fulton, Robert S., Ramakrishnan, Sai Mukund, Chang, Gue Su, Petti, Allegra A., Spencer, David H., Miller, Christopher A., and Ley, Timothy J.

Published
2020

27. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

Author

Farshidfar, Farshad, Zheng, Siyuan, Gingras, Marie-Claude, Newton, Yulia, Shih, Juliann, Robertson, A Gordon, Hinoue, Toshinori, Hoadley, Katherine A, Gibb, Ewan A, Roszik, Jason, Covington, Kyle R, Wu, Chia-Chin, Shinbrot, Eve, Stransky, Nicolas, Hegde, Apurva, Yang, Ju Dong, Reznik, Ed, Sadeghi, Sara, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I, Hess, Julian M, Auman, J Todd, Rhie, Suhn K, Bowlby, Reanne, Borad, Mitesh J, Network, The Cancer Genome Atlas, Akbani, Rehan, Allotey, Loretta K, Ally, Adrian, Alvaro, Domenico, Andersen, Jesper B, Appelbaum, Elizabeth L, Arora, Arshi, Balasundaram, Miruna, Balu, Saianand, Bardeesy, Nabeel, Bathe, Oliver F, Baylin, Stephen B, Beroukhim, Rameen, Berrios, Mario, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S, Bowen, Jay, Bragazzi, Maria Consiglia, Brooks, Denise, Cardinale, Vincenzo, Carlsen, Rebecca, Carpino, Guido, Carvalho, Andre L, Chaiteerakij, Roongruedee, Chandan, Vishal C, Cherniack, Andrew D, Chin, Lynda, Cho, Juok, Choe, Gina, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cordes, Matthew G, Crain, Daniel, Curley, Erin, De Rose, Agostino Maria, Defreitas, Timothy, Demchok, John A, Deshpande, Vikram, Dhalla, Noreen, Ding, Li, Evason, Kimberley, Felau, Ina, Ferguson, Martin L, Foo, Wai Chin, Franchitto, Antonio, Frazer, Scott, Fronick, Catrina C, Fulton, Lucinda A, Fulton, Robert S, Gabriel, Stacey B, Gardner, Johanna, Gastier-Foster, Julie M, Gaudio, Eugenio, Gehlenborg, Nils, Genovese, Giannicola, Gerken, Mark, Getz, Gad, Giama, Nasra H, Gibbs, Richard A, Giuliante, Felice, Grazi, Gian Luca, Hayes, D Neil, Hegde, Apurva M, and Heiman, David I

Subjects
Liver Cancer, Digestive Diseases, Liver Disease, Biotechnology, Human Genome, Genetics, Cancer, Rare Diseases, Digestive Diseases - (Gallbladder), Adult, Aged, Aged, 80 and over, Bile Duct Neoplasms, Cholangiocarcinoma, Chromatin, DNA Methylation, DNA-Binding Proteins, Female, Gene Expression Regulation, Neoplastic, Genomics, Humans, Isocitrate Dehydrogenase, Liver, Liver Neoplasms, Male, Middle Aged, Mitochondria, Mutation, Nuclear Proteins, Pancreatic Neoplasms, Promoter Regions, Genetic, RNA, Long Noncoding, RNA, Messenger, Transcription Factors, Cancer Genome Atlas Network, ARID1A, DNA methylation, IDH, RNA sequencing, TCGA, cholangiocarcinoma, integrative genomics, lncRNAs, multi-omics, whole exome, Biochemistry and Cell Biology, Medical Physiology
Abstract

Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

Published
2017

28. Integrated genomic and molecular characterization of cervical cancer

Author

Burk, Robert D, Chen, Zigui, Saller, Charles, Tarvin, Katherine, Carvalho, Andre L, Scapulatempo-Neto, Cristovam, Silveira, Henrique C, Fregnani, José H, Creighton, Chad J, Anderson, Matthew L, Castro, Patricia, Wang, Sophia S, Yau, Christina, Benz, Christopher, Robertson, A Gordon, Mungall, Karen, Lim, Lynette, Bowlby, Reanne, Sadeghi, Sara, Brooks, Denise, Sipahimalani, Payal, Mar, Richard, Ally, Adrian, Clarke, Amanda, Mungall, Andrew J, Tam, Angela, Lee, Darlene, Chuah, Eric, Schein, Jacqueline E, Tse, Kane, Kasaian, Katayoon, Ma, Yussanne, Marra, Marco A, Mayo, Michael, Balasundaram, Miruna, Thiessen, Nina, Dhalla, Noreen, Carlsen, Rebecca, Moore, Richard A, Holt, Robert A, Jones, Steven JM, Wong, Tina, Pantazi, Angeliki, Parfenov, Michael, Kucherlapati, Raju, Hadjipanayis, Angela, Seidman, Jonathan, Kucherlapati, Melanie, Ren, Xiaojia, Xu, Andrew W, Yang, Lixing, Park, Peter J, Lee, Semin, Rabeno, Brenda, Huelsenbeck-Dill, Lori, Borowsky, Mark, Cadungog, Mark, Iacocca, Mary, Petrelli, Nicholas, Swanson, Patricia, Ojesina, Akinyemi I, Le, Xuan, Sandusky, George, Adebamowo, Sally N, Akeredolu, Teniola, Adebamowo, Clement, Reynolds, Sheila M, Shmulevich, Ilya, Shelton, Candace, Crain, Daniel, Mallery, David, Curley, Erin, Gardner, Johanna, Penny, Robert, Morris, Scott, Shelton, Troy, Liu, Jia, Lolla, Laxmi, Chudamani, Sudha, Wu, Ye, Birrer, Michael, McLellan, Michael D, Bailey, Matthew H, Miller, Christopher A, Wyczalkowski, Matthew A, Fulton, Robert S, Fronick, Catrina C, Lu, Charles, Mardis, Elaine R, Appelbaum, Elizabeth L, Schmidt, Heather K, Fulton, Lucinda A, Cordes, Matthew G, Li, Tiandao, Ding, Li, Wilson, Richard K, Rader, Janet S, Behmaram, Behnaz, Uyar, Denise, and Bradley, William

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Cervical Cancer, Cancer, Clinical Research, Human Genome, Sexually Transmitted Infections, Biotechnology, Genetics, 2.1 Biological and endogenous factors, Aetiology, APOBEC-1 Deaminase, Adenocarcinoma, B7-H1 Antigen, Carcinoma, Squamous Cell, Caspase 8, DNA-Binding Proteins, Female, Genomics, HLA-A Antigens, Human papillomavirus 16, Humans, Keratins, Mitogen-Activated Protein Kinase Kinases, Molecular Targeted Therapy, Mutation, Nuclear Proteins, PTEN Phosphohydrolase, Phosphatidylinositol 3-Kinases, Programmed Cell Death 1 Ligand 2 Protein, Protein Serine-Threonine Kinases, Proteomics, Proto-Oncogene Proteins p21(ras), RNA, Long Noncoding, Receptor, ErbB-3, Receptor, Transforming Growth Factor-beta Type II, Receptors, Transforming Growth Factor beta, Signal Transduction, Transcription Factors, Uterine Cervical Neoplasms, Virus Integration, Cancer Genome Atlas Research Network, Albert Einstein College of Medicine, Analytical Biological Services, Barretos Cancer Hospital, Baylor College of Medicine, Beckman Research Institute of City of Hope, Buck Institute for Research on Aging, Canada's Michael Smith Genome Sciences Centre, Harvard Medical School, Helen F. Graham Cancer Center &Research Institute at Christiana Care Health Services, HudsonAlpha Institute for Biotechnology, ILSbio, LLC, Indiana University School of Medicine, Institute of Human Virology, Institute for Systems Biology, International Genomics Consortium, Leidos Biomedical, Massachusetts General Hospital, McDonnell Genome Institute at Washington University, Medical College of Wisconsin, Medical University of South Carolina, Memorial Sloan Kettering Cancer Center, Montefiore Medical Center, NantOmics, National Cancer Institute, National Hospital, Abuja, Nigeria, National Human Genome Research Institute, National Institute of Environmental Health Sciences, National Institute on Deafness &Other Communication Disorders, Ontario Tumour Bank, London Health Sciences Centre, Ontario Tumour Bank, Ontario Institute for Cancer Research, Ontario Tumour Bank, The Ottawa Hospital, Oregon Health &Science University, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, SRA International, St Joseph's Candler Health System, Eli &Edythe L. Broad Institute of Massachusetts Institute of Technology &Harvard University, Research Institute at Nationwide Children's Hospital, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, University of Bergen, University of Texas MD Anderson Cancer Center, University of Abuja Teaching Hospital, University of Alabama at Birmingham, University of California, Irvine, University of California Santa Cruz, University of Kansas Medical Center, University of Lausanne, University of New Mexico Health Sciences Center, University of North Carolina at Chapel Hill, University of Oklahoma Health Sciences Center, University of Pittsburgh, University of São Paulo, Ribeir ão Preto Medical School, University of Southern California, University of Washington, University of Wisconsin School of Medicine &Public Health, Van Andel Research Institute, Washington University in St Louis, Receptor, erbB-3, General Science & Technology
Abstract

Cervical cancer remains one of the leading causes of cancer-related deaths worldwide. Here we report the extensive molecular characterization of 228 primary cervical cancers, one of the largest comprehensive genomic studies of cervical cancer to date. We observed notable APOBEC mutagenesis patterns and identified SHKBP1, ERBB3, CASP8, HLA-A and TGFBR2 as novel significantly mutated genes in cervical cancer. We also discovered amplifications in immune targets CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2), and the BCAR4 long non-coding RNA, which has been associated with response to lapatinib. Integration of human papilloma virus (HPV) was observed in all HPV18-related samples and 76% of HPV16-related samples, and was associated with structural aberrations and increased target-gene expression. We identified a unique set of endometrial-like cervical cancers, comprised predominantly of HPV-negative tumours with relatively high frequencies of KRAS, ARID1A and PTEN mutations. Integrative clustering of 178 samples identified keratin-low squamous, keratin-high squamous and adenocarcinoma-rich subgroups. These molecular analyses reveal new potential therapeutic targets for cervical cancers.

Published
2017

29. Human whole-exome genotype data for Alzheimer’s disease

Author

Leung, Yuk Yee, Naj, Adam C., Chou, Yi Fan, Valladares, Otto, Schmidt, Michael, Hamilton-Nelson, Kara, Wheeler, Nicholas, Lin, Honghuang, Gangadharan, Prabhakaran, Qu, Liming, Clark, Kaylyn, Kuzma, Amanda B., Lee, Wan Ping, Cantwell, Laura, Nicaretta, Heather, van der Lee, Sven, English, Adam, Kalra, Divya, Muzny, Donna, Skinner, Evette, Doddapeneni, Harsha, Dinh, Huyen, Hu, Jianhong, Santibanez, Jireh, Jayaseelan, Joy, Worley, Kim, Gibbs, Richard A., Lee, Sandra, Dugan-Perez, Shannon, Korchina, Viktoriya, Nasser, Waleed, Liu, Xiuping, Han, Yi, Zhu, Yiming, Liu, Yue, Khan, Ziad, Zhu, Congcong, Sun, Fangui Jenny, Jun, Gyungah R., Chung, Jaeyoon, Farrell, John, Zhang, Xiaoling, Banks, Eric, Gupta, Namrata, Gabriel, Stacey, Butkiewicz, Mariusz, Benchek, Penelope, Smieszek, Sandra, Song, Yeunjoo, Vardarajan, Badri, Reitz, Christiane, Reyes-Dumeyer, Dolly, Tosto, Giuseppe, De Jager, Phillip L., Barral, Sandra, Ma, Yiyi, Beiser, Alexa, Liu, Ching Ti, Dupuis, Josee, Lunetta, Kathy, Cupples, L. Adrienne, Choi, Seung Hoan, Chen, Yuning, Mez, Jesse, Vanderspek, Ashley, Ikram, M. Arfan, Ahmad, Shahzad, Faber, Kelley, Foroud, Tatiana, Mlynarski, Elisabeth, Schmidt, Helena, Schmidt, Reinhold, Kunkle, Brian, Rajabli, Farid, Beecham, Gary, Vance, Jeffrey M., Adams, Larry D., Cuccaro, Michael, Mena, Pedro, Booth, Briana M., Renton, Alan, Goate, Alison, Marcora, Edoardo, Stine, Adam, Feolo, Michael, Launer, Lenore J., Koboldt, Daniel C., Wilson, Richard K., van Duijn, Cornelia, Amin, Najaf, Kapoor, Manav, Salerno, William, Bennett, David A., Xia, Li Charlie, Malamon, John, Mosley, Thomas H., Satizabal, Claudia, Jan Bressler, Bressler, Jian, Xueqiu, Nato, Alejandro Q., Horimoto, Andrea R., Wang, Bowen, Psaty, Bruce, Witten, Daniela, Tsuang, Debby, Blue, Elizabeth, Wijsman, Ellen, Sohi, Harkirat, Nguyen, Hiep, Bis, Joshua C., Rice, Kenneth, Brown, Lisa, Dorschner, Michael, Saad, Mohamad, Navas, Pat, Nafikov, Rafael, Thornton, Timothy, Day, Tyler, Haut, Jacob, Sha, Jin, Zhang, Nancy, Iqbal, Taha, Zhao, Yi, Below, Jennifer E., Larson, David E., Appelbaum, Elizabeth, Waligorski, Jason, Antonacci-Fulton, Lucinda, Fulton, Robert S., Haines, Jonathan, Farrer, Lindsay, Seshadri, Sudha, Brkanac, Zoran, Cruchaga, Carlos, Pericak-Vance, Margaret, Mayeux, Richard P., Bush, William S., Destefano, Anita, Martin, Eden, Schellenberg, Gerard D., Wang, Li San, Leung, Yuk Yee, Naj, Adam C., Chou, Yi Fan, Valladares, Otto, Schmidt, Michael, Hamilton-Nelson, Kara, Wheeler, Nicholas, Lin, Honghuang, Gangadharan, Prabhakaran, Qu, Liming, Clark, Kaylyn, Kuzma, Amanda B., Lee, Wan Ping, Cantwell, Laura, Nicaretta, Heather, van der Lee, Sven, English, Adam, Kalra, Divya, Muzny, Donna, Skinner, Evette, Doddapeneni, Harsha, Dinh, Huyen, Hu, Jianhong, Santibanez, Jireh, Jayaseelan, Joy, Worley, Kim, Gibbs, Richard A., Lee, Sandra, Dugan-Perez, Shannon, Korchina, Viktoriya, Nasser, Waleed, Liu, Xiuping, Han, Yi, Zhu, Yiming, Liu, Yue, Khan, Ziad, Zhu, Congcong, Sun, Fangui Jenny, Jun, Gyungah R., Chung, Jaeyoon, Farrell, John, Zhang, Xiaoling, Banks, Eric, Gupta, Namrata, Gabriel, Stacey, Butkiewicz, Mariusz, Benchek, Penelope, Smieszek, Sandra, Song, Yeunjoo, Vardarajan, Badri, Reitz, Christiane, Reyes-Dumeyer, Dolly, Tosto, Giuseppe, De Jager, Phillip L., Barral, Sandra, Ma, Yiyi, Beiser, Alexa, Liu, Ching Ti, Dupuis, Josee, Lunetta, Kathy, Cupples, L. Adrienne, Choi, Seung Hoan, Chen, Yuning, Mez, Jesse, Vanderspek, Ashley, Ikram, M. Arfan, Ahmad, Shahzad, Faber, Kelley, Foroud, Tatiana, Mlynarski, Elisabeth, Schmidt, Helena, Schmidt, Reinhold, Kunkle, Brian, Rajabli, Farid, Beecham, Gary, Vance, Jeffrey M., Adams, Larry D., Cuccaro, Michael, Mena, Pedro, Booth, Briana M., Renton, Alan, Goate, Alison, Marcora, Edoardo, Stine, Adam, Feolo, Michael, Launer, Lenore J., Koboldt, Daniel C., Wilson, Richard K., van Duijn, Cornelia, Amin, Najaf, Kapoor, Manav, Salerno, William, Bennett, David A., Xia, Li Charlie, Malamon, John, Mosley, Thomas H., Satizabal, Claudia, Jan Bressler, Bressler, Jian, Xueqiu, Nato, Alejandro Q., Horimoto, Andrea R., Wang, Bowen, Psaty, Bruce, Witten, Daniela, Tsuang, Debby, Blue, Elizabeth, Wijsman, Ellen, Sohi, Harkirat, Nguyen, Hiep, Bis, Joshua C., Rice, Kenneth, Brown, Lisa, Dorschner, Michael, Saad, Mohamad, Navas, Pat, Nafikov, Rafael, Thornton, Timothy, Day, Tyler, Haut, Jacob, Sha, Jin, Zhang, Nancy, Iqbal, Taha, Zhao, Yi, Below, Jennifer E., Larson, David E., Appelbaum, Elizabeth, Waligorski, Jason, Antonacci-Fulton, Lucinda, Fulton, Robert S., Haines, Jonathan, Farrer, Lindsay, Seshadri, Sudha, Brkanac, Zoran, Cruchaga, Carlos, Pericak-Vance, Margaret, Mayeux, Richard P., Bush, William S., Destefano, Anita, Martin, Eden, Schellenberg, Gerard D., and Wang, Li San

Abstract

The heterogeneity of the whole-exome sequencing (WES) data generation methods present a challenge to a joint analysis. Here we present a bioinformatics strategy for joint-calling 20,504 WES samples collected across nine studies and sequenced using ten capture kits in fourteen sequencing centers in the Alzheimer’s Disease Sequencing Project. The joint-genotype called variant-called format (VCF) file contains only positions within the union of capture kits. The VCF was then processed specifically to account for the batch effects arising from the use of different capture kits from different studies. We identified 8.2 million autosomal variants. 96.82% of the variants are high-quality, and are located in 28,579 Ensembl transcripts. 41% of the variants are intronic and 1.8% of the variants are with CADD > 30, indicating they are of high predicted pathogenicity. Here we show our new strategy can generate high-quality data from processing these diversely generated WES samples. The improved ability to combine data sequenced in different batches benefits the whole genomics research community.

Published
2024

30. Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma

Author

Gomez, Felicia, primary, Fisk, Bryan, additional, McMichael, Joshua F., additional, Mosior, Matthew, additional, Foltz, Jennifer A., additional, Skidmore, Zachary L., additional, Duncavage, Eric J., additional, Miller, Christopher A., additional, Abel, Haley, additional, Li, Yi-Shan, additional, Russler-Germain, David A., additional, Krysiak, Kilannin, additional, Watkins, Marcus P., additional, Ramirez, Cody A., additional, Schmidt, Alina, additional, Martins Rodrigues, Fernanda, additional, Trani, Lee, additional, Khanna, Ajay, additional, Wagner, Julia A., additional, Fulton, Robert S., additional, Fronick, Catrina C., additional, O'Laughlin, Michelle D., additional, Schappe, Timothy, additional, Cashen, Amanda F., additional, Mehta-Shah, Neha, additional, Kahl, Brad S., additional, Walker, Jason, additional, Bartlett, Nancy L., additional, Griffith, Malachi, additional, Fehniger, Todd A., additional, and Griffith, Obi L., additional

Published
2023
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31. Supplementary Figure 5 from Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma

Author

Gomez, Felicia, primary, Fisk, Bryan, primary, McMichael, Joshua F., primary, Mosior, Matthew, primary, Foltz, Jennifer A., primary, Skidmore, Zachary L., primary, Duncavage, Eric J., primary, Miller, Christopher A., primary, Abel, Haley, primary, Li, Yi-Shan, primary, Russler-Germain, David A., primary, Krysiak, Kilannin, primary, Watkins, Marcus P., primary, Ramirez, Cody A., primary, Schmidt, Alina, primary, Martins Rodrigues, Fernanda, primary, Trani, Lee, primary, Khanna, Ajay, primary, Wagner, Julia A., primary, Fulton, Robert S., primary, Fronick, Catrina C., primary, O'Laughlin, Michelle D., primary, Schappe, Timothy, primary, Cashen, Amanda F., primary, Mehta-Shah, Neha, primary, Kahl, Brad S., primary, Walker, Jason, primary, Bartlett, Nancy L., primary, Griffith, Malachi, primary, Fehniger, Todd A., primary, and Griffith, Obi L., primary

Published
2023
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32. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages

Author

Iglesia, Michael D., primary, Jayasinghe, Reyka G., additional, Chen, Siqi, additional, Terekhanova, Nadezhda V., additional, Herndon, John M., additional, Storrs, Erik, additional, Karpova, Alla, additional, Zhou, Daniel Cui, additional, Al Deen, Nataly Naser, additional, Shinkle, Andrew T., additional, Lu, Rita Jui-Hsien, additional, Caravan, Wagma, additional, Houston, Andrew, additional, Zhao, Yanyan, additional, Sato, Kazuhito, additional, Lal, Preet, additional, Street, Cherease, additional, Rodrigues, Fernanda Martins, additional, Southard-Smith, Austin N., additional, Targino da Costa, André Luiz N., additional, Zhu, Houxiang, additional, Mo, Chia-Kuei, additional, Crowson, Lisa, additional, Fulton, Robert S., additional, Wyczalkowski, Matthew A., additional, Fronick, Catrina C., additional, Fulton, Lucinda A., additional, Sun, Hua, additional, Davies, Sherri R., additional, Appelbaum, Elizabeth L., additional, Chasnoff, Sara E., additional, Carmody, Madelyn, additional, Brooks, Candace, additional, Liu, Ruiyang, additional, Wendl, Michael C., additional, Oh, Clara, additional, Bender, Diane, additional, Cruchaga, Carlos, additional, Harari, Oscar, additional, Bredemeyer, Andrea, additional, Lavine, Kory, additional, Bose, Ron, additional, Margenthaler, Julie, additional, Held, Jason M., additional, Achilefu, Samuel, additional, Ademuyiwa, Foluso, additional, Aft, Rebecca, additional, Ma, Cynthia, additional, Colditz, Graham A., additional, Ju, Tao, additional, Oh, Stephen T., additional, Fitzpatrick, James, additional, Hwang, E. Shelley, additional, Shoghi, Kooresh I., additional, Chheda, Milan G., additional, Veis, Deborah J., additional, Chen, Feng, additional, Fields, Ryan C., additional, Gillanders, William E., additional, and Ding, Li, additional

Published
2023
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33. 6. Tracking immunotherapy response with single cell T cell receptor profiling in canine models of cancer

Author

Griffith, Obi, primary, Skidmore, Zachary, additional, Rindt, Hans, additional, Chu, Shirley, additional, Fisk, Bryan, additional, Hoang, My, additional, Fronick, Catrina, additional, Fulton, Robert, additional, Zhou, Mingyi, additional, Bivens, Nathan, additional, Reinero, Carol, additional, Griffith, Malachi, additional, and Bryan, Jeff, additional

Published
2023
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34. Germline genetic variation in ETV6 and risk of childhood acute lymphoblastic leukaemia: a systematic genetic study

Author

Moriyama, Takaya, Metzger, Monika L, Wu, Gang, Nishii, Rina, Qian, Maoxiang, Devidas, Meenakshi, Yang, Wenjian, Cheng, Cheng, Cao, Xueyuan, Quinn, Emily, Raimondi, Susana, Gastier-Foster, Julie M, Raetz, Elizabeth, Larsen, Eric, Martin, Paul L, Bowman, W Paul, Winick, Naomi, Komada, Yoshihiro, Wang, Shuoguo, Edmonson, Michael, Xu, Heng, Mardis, Elaine, Fulton, Robert, Pui, Ching-Hon, Mullighan, Charles, Evans, William E, Zhang, Jinghui, Hunger, Stephen P, Relling, Mary V, Nichols, Kim E, Loh, Mignon L, and Yang, Jun J

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetic Testing, Hematology, Human Genome, Clinical Research, Cancer, Childhood Leukemia, Genetics, Pediatric Cancer, Rare Diseases, Pediatric, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Age Factors, Biomarkers, Tumor, Case-Control Studies, Child, Child, Preschool, Computational Biology, DNA Mutational Analysis, Databases, Genetic, Exome, Female, Gene Frequency, Genetic Association Studies, Genetic Predisposition to Disease, Germ-Line Mutation, Humans, Karyotyping, Male, Phenotype, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Proto-Oncogene Proteins c-ets, Repressor Proteins, Risk Factors, Treatment Outcome, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

BackgroundHereditary predisposition is rarely suspected for childhood acute lymphoblastic leukaemia (ALL). Recent reports of germline ETV6 variations associated with substantial familial clustering of haematological malignancies indicated that this gene is a potentially important genetic determinant for ALL susceptibility. Our aims in this study were to comprehensively identify ALL predisposition variants in ETV6 and to determine the extent to which they contributed to the overall risk of childhood ALL.MethodsWhole-exome sequencing of an index family with several cases of ALL was done to identify causal variants for ALL predisposition. Targeted sequencing of ETV6 was done in children from the Children's Oncology Group and St Jude Children's Research Hospital front-line ALL trials. Patients were included in this study on the basis of their enrolment in these clinical trials and the availability of germline DNA. ETV6 variant genotypes were compared with non-ALL controls to define ALL-related germline risk variants. ETV6 variant function was characterised bioinformatically and correlated with clinical and demographic features in children with ALL.FindingsWe identified a novel non-sense ETV6 variant (p.Arg359X) with a high penetrance in an index family. Subsequent targeted sequencing of ETV6 in 4405 childhood ALL cases identified 31 exonic variants (four non-sense, 21 missense, one splice site, and five frameshift variants) that were potentially related to ALL risk in 35 cases (1%). 15 (48%) of 31 ALL-related ETV6 variants clustered in the erythroblast transformation specific domain and were predicted to be highly deleterious. Children with ALL-related ETV6 variants were significantly older at leukaemia diagnosis than those without (10·2 years [IQR 5·3-13·8] vs 4·7 years [3·0-8·7]; p=0·017). The hyperdiploid leukaemia karyotype was highly over-represented in ALL cases harbouring germline ETV6 risk variants compared with the wild-type group (nine [64%] of 14 cases vs 538 [27%] of 2007 cases; p=0·0050).InterpretationOur findings indicated germline ETV6 variations as the basis of a novel genetic syndrome associated with predisposition to childhood ALL. The development of recommendations for clinical interventions and surveillance for individuals harbouring ALL-related ETV6 variants are needed.FundingUS National Institutes of Health and American Lebanese Syrian Associated Charities.

Published
2015

35. Co-evolution of tumor and immune cells during progression of multiple myeloma

Author

Liu, Ruiyang, Gao, Qingsong, Foltz, Steven M., Fowles, Jared S., Yao, Lijun, Wang, Julia Tianjiao, Cao, Song, Sun, Hua, Wendl, Michael C., Sethuraman, Sunantha, Weerasinghe, Amila, Rettig, Michael P., Storrs, Erik P., Yoon, Christopher J., Wyczalkowski, Matthew A., McMichael, Joshua F., Kohnen, Daniel R., King, Justin, Goldsmith, Scott R., O’Neal, Julie, Fulton, Robert S., Fronick, Catrina C., Ley, Timothy J., Jayasinghe, Reyka G., Fiala, Mark A., Oh, Stephen T., DiPersio, John F., Vij, Ravi, and Ding, Li

Published
2021
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36. Author Correction: Comparative and demographic analysis of orang-utan genomes

Author

Locke, Devin P., Hillier, LaDeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Della Valle, Giuliano, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, de Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., and Wilson, Richard K.

Published
2022
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37. Whole Exome Sequencing Reveals the Order of Genetic Changes during Malignant Transformation and Metastasis in a Single Patient with NF1-plexiform Neurofibroma

Author

Hirbe, Angela C, Dahiya, Sonika, Miller, Christopher A, Li, Tiandao, Fulton, Robert S, Zhang, Xiaochun, McDonald, Sandra, DeSchryver, Katherine, Duncavage, Eric J, Walrath, Jessica, Reilly, Karlyne M, Abel, Haley J, Pekmezci, Melike, Perry, Arie, Ley, Timothy J, and Gutmann, David H

Subjects
Biotechnology, Cancer, Human Genome, Genetics, Pediatric, Neurofibromatosis, Rare Diseases, Neurosciences, Aetiology, 2.1 Biological and endogenous factors, Animals, Biopsy, Cell Transformation, Neoplastic, DNA Copy Number Variations, Disease Progression, Exome, Genes, p53, Genetic Variation, Humans, Mice, Mutation, Neoplasm Metastasis, Neoplasm Transplantation, Nerve Sheath Neoplasms, Neurofibroma, Plexiform, Neurofibromatosis 1, Oligonucleotide Array Sequence Analysis, Sequence Analysis, DNA, Spectrin, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

PurposeMalignant peripheral nerve sheath tumors (MPNST) occur at increased frequency in individuals with neurofibromatosis type 1 (NF1), where they likely arise from benign plexiform neurofibroma precursors. While previous studies have used a variety of discovery approaches to discover genes associated with MPNST pathogenesis, it is currently unclear what molecular events are associated with the evolution of MPNST from plexiform neurofibroma.Experimental designWhole-exome sequencing was performed on biopsy materials representing plexiform neurofibroma (n = 3), MPNST, and metastasis from a single individual with NF1 over a 14-year period. Additional validation cases were used to assess candidate genes involved in malignant progression, while a murine MPNST model was used for functional analysis.ResultsThere was an increasing proportion of cells with a somatic NF1 gene mutation as the tumors progressed from benign to malignant, suggesting a clonal process in MPNST development. Copy number variations, including loss of one copy of the TP53 gene, were identified in the primary tumor and the metastatic lesion, but not in benign precursor lesions. A limited number of genes with nonsynonymous somatic mutations (βIII-spectrin and ZNF208) were discovered, several of which were validated in additional primary and metastatic MPNST samples. Finally, increased βIII-spectrin expression was observed in the majority of MPNSTs, and shRNA-mediated knockdown reduced murine MPNST growth in vivo.ConclusionsCollectively, the ability to track the molecular evolution of MPNST in a single individual with NF1 offers new insights into the sequence of genetic events important for disease pathogenesis and progression for future mechanistic study.

Published
2015

38. Inherited coding variants at the CDKN2A locus influence susceptibility to acute lymphoblastic leukaemia in children.

Author

Xu, Heng, Zhang, Hui, Yang, Wenjian, Yadav, Rachita, Morrison, Alanna C, Qian, Maoxiang, Devidas, Meenakshi, Liu, Yu, Perez-Andreu, Virginia, Zhao, Xujie, Gastier-Foster, Julie M, Lupo, Philip J, Neale, Geoff, Raetz, Elizabeth, Larsen, Eric, Bowman, W Paul, Carroll, William L, Winick, Naomi, Williams, Richard, Hansen, Torben, Holm, Jens-Christian, Mardis, Elaine, Fulton, Robert, Pui, Ching-Hon, Zhang, Jinghui, Mullighan, Charles G, Evans, William E, Hunger, Stephen P, Gupta, Ramneek, Schmiegelow, Kjeld, Loh, Mignon L, Relling, Mary V, and Yang, Jun J

Subjects
Hematopoietic Stem Cells, Animals, Humans, Mice, Genetic Predisposition to Disease, DNA-Binding Proteins, Transcription Factors, Case-Control Studies, Mutagenesis, Site-Directed, Genotype, Germ-Line Mutation, Mutation, Missense, Child, Cyclin-Dependent Kinase Inhibitor p16, Cyclin-Dependent Kinase Inhibitor p15, Ikaros Transcription Factor, Precursor B-Cell Lymphoblastic Leukemia-Lymphoma, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Genetic Variation, Genome-Wide Association Study, HEK293 Cells, Mutagenesis, Site-Directed, Mutation, Missense
Abstract

There is increasing evidence from genome-wide association studies for a strong inherited genetic basis of susceptibility to acute lymphoblastic leukaemia (ALL) in children, yet the effects of protein-coding variants on ALL risk have not been systematically evaluated. Here we show a missense variant in CDKN2A associated with the development of ALL at genome-wide significance (rs3731249, P=9.4 × 10(-23), odds ratio=2.23). Functional studies indicate that this hypomorphic variant results in reduced tumour suppressor function of p16(INK4A), increases the susceptibility to leukaemic transformation of haematopoietic progenitor cells, and is preferentially retained in ALL tumour cells. Resequencing the CDKN2A-CDKN2B locus in 2,407 childhood ALL cases reveals 19 additional putative functional germline variants. These results provide direct functional evidence for the influence of inherited genetic variation on ALL risk, highlighting the important and complex roles of CDKN2A-CDKN2B tumour suppressors in leukaemogenesis.

Published
2015

40. Pediatric ADHD med errors prompt call for prevention

Author

Fulton, Robert

Subjects
Pediatrics -- Reports -- Health aspects, Medication errors -- Health aspects -- Reports, Attention-deficit hyperactivity disorder -- Prevention, Health, Health care industry, Psychology and mental health
Abstract

The frequency of medication errors among children who take drugs to treat attention-deficit/ hyperactivity disorder reported to U.S. poison control centers increased by nearly 300% over a 22year period, according [...]

Published
2023

41. A rare missense variant of CASP7 is associated with familial late-onset Alzheimer's disease

Author

Bellair, Michelle, Dinh, Huyen, Doddapeneni, Harsha, Dugan-Perez, Shannon, English, Adam, Gibbs, Richard A., Han, Yi, Hu, Jianhong, Jayaseelan, Joy, Kalra, Divya, Khan, Ziad, Korchina, Viktoriya, Lee, Sandra, Liu, Yue, Liu, Xiuping, Muzny, Donna, Nasser, Waleed, Salerno, William, Santibanez, Jireh, Skinner, Evette, White, Simon, Worley, Kim, Zhu, Yiming, Beiser, Alexa, Chen, Yuning, Chung, Jaeyoon, Cupples, L. Adrienne, DeStefano, Anita, Dupuis, Josee, Farrell, John, Farrer, Lindsay, Lancour, Daniel, Lin, Honghuang, Liu, Ching Ti, Lunetta, Kathy, Ma, Yiyi, Patel, Devanshi, Sarnowski, Chloe, Satizabal, Claudia, Seshadri, Sudha, Sun, Fangui Jenny, Zhang, Xiaoling, Choi, Seung Hoan, Banks, Eric, Gabriel, Stacey, Gupta, Namrata, Bush, William, Butkiewicz, Mariusz, Haines, Jonathan, Smieszek, Sandra, Song, Yeunjoo, Barral, Sandra, De Jager, Phillip L., Mayeux, Richard, Reitz, Christiane, Reyes, Dolly, Tosto, Giuseppe, Vardarajan, Badri, Amad, Shahzad, Amin, Najaf, Ikram, M. Afran, van der Lee, Sven, van Duijn, Cornelia, Vanderspek, Ashley, Schmidt, Helena, Schmidt, Reinhold, Goate, Alison, Kapoor, Manav, Marcora, Edoardo, Renton, Alan, Faber, Kelley, Foroud, Tatiana, Feolo, Michael, Stine, Adam, Launer, Lenore J., Bennett, David A., Xia, Li Charlie, Beecham, Gary, Hamilton-Nelson, Kara, Jaworski, James, Kunkle, Brian, Martin, Eden, Pericak-Vance, Margaret, Rajabli, Farid, Schmidt, Michael, Mosley, Thomas H., Cantwell, Laura, Childress, Micah, Chou, Yi-Fan, Cweibel, Rebecca, Gangadharan, Prabhakaran, Kuzma, Amanda, Leung, Yuk Yee, Lin, Han-Jen, Malamon, John, Mlynarski, Elisabeth, Naj, Adam, Qu, Liming, Schellenberg, Gerard, Valladares, Otto, Wang, Li-San, Wang, Weixin, Zhang, Nancy, Below, Jennifer E., Boerwinkle, Eric, Bressler, Jan, Fornage, Myriam, Jian, Xueqiu, Liu, Xiaoming, Bis, Joshua C., Blue, Elizabeth, Brown, Lisa, Day, Tyler, Dorschner, Michael, Horimoto, Andrea R., Nafikov, Rafael, Nato, Alejandro Q., Jr., Navas, Pat, Nguyen, Hiep, Psaty, Bruce, Rice, Kenneth, Saad, Mohamad, Sohi, Harkirat, Thornton, Timothy, Tsuang, Debby, Wang, Bowen, Wijsman, Ellen, Witten, Daniela, Antonacci-Fulton, Lucinda, Appelbaum, Elizabeth, Cruchaga, Carlos, Fulton, Robert S., Koboldt, Daniel C., Larson, David E., Waligorski, Jason, Wilson, Richard K., Zhu, Congcong, Vardarajan, Badri N., Farrell, John J., Haines, Jonathan L., Schellenberg, Gerard D., Pericak-Vance, Margaret A., Lunetta, Kathryn L., and Farrer, Lindsay A.

Published
2019
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43. Study: Prenatal supplements fail to meet nutrient needs

Author

Fulton, Robert

Subjects
Dietary supplements -- Reports -- Research, College teachers -- Reports -- Research, Pregnant women -- Research -- Reports, Health
Abstract

Although drugstore shelves might suggest otherwise, affordable dietary supplements that provide critical nutrients in appropriate doses for pregnant women are virtually nonexistent, researchers have found. In a new study published [...]

Published
2023

44. Comprehensive molecular profiling of lung adenocarcinoma

Author

Collisson, Eric A, Campbell, Joshua D, Brooks, Angela N, Berger, Alice H, Lee, William, Chmielecki, Juliann, Beer, David G, Cope, Leslie, Creighton, Chad J, Danilova, Ludmila, Ding, Li, Getz, Gad, Hammerman, Peter S, Neil Hayes, D, Hernandez, Bryan, Herman, James G, Heymach, John V, Jurisica, Igor, Kucherlapati, Raju, Kwiatkowski, David, Ladanyi, Marc, Robertson, Gordon, Schultz, Nikolaus, Shen, Ronglai, Sinha, Rileen, Sougnez, Carrie, Tsao, Ming-Sound, Travis, William D, Weinstein, John N, Wigle, Dennis A, Wilkerson, Matthew D, Chu, Andy, Cherniack, Andrew D, Hadjipanayis, Angela, Rosenberg, Mara, Weisenberger, Daniel J, Laird, Peter W, Radenbaugh, Amie, Ma, Singer, Stuart, Joshua M, Averett Byers, Lauren, Baylin, Stephen B, Govindan, Ramaswamy, Meyerson, Matthew, Gabriel, Stacey B, Cibulskis, Kristian, Kim, Jaegil, Stewart, Chip, Lichtenstein, Lee, Lander, Eric S, Lawrence, Michael S, Kandoth, Cyriac, Fulton, Robert, Fulton, Lucinda L, McLellan, Michael D, Wilson, Richard K, Ye, Kai, Fronick, Catrina C, Maher, Christopher A, Miller, Christopher A, Wendl, Michael C, Cabanski, Christopher, Mardis, Elaine, Wheeler, David, Balasundaram, Miruna, Butterfield, Yaron SN, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Lee, Darlene, Li, Haiyan I, Mayo, Michael, Moore, Richard A, Mungall, Andrew J, Schein, Jacqueline E, Sipahimalani, Payal, Tam, Angela, Varhol, Richard, Gordon Robertson, A, Wye, Natasja, Thiessen, Nina, Holt, Robert A, Jones, Steven JM, Marra, Marco A, Imielinski, Marcin, Onofrio, Robert C, Hodis, Eran, and Zack, Travis

Subjects
Rare Diseases, Genetics, Biotechnology, Clinical Research, Lung Cancer, Human Genome, Cancer, Lung, Aetiology, 2.1 Biological and endogenous factors, Adenocarcinoma, Adenocarcinoma of Lung, Cell Cycle Proteins, Female, Gene Dosage, Gene Expression Regulation, Neoplastic, Genomics, Humans, Lung Neoplasms, Male, Molecular Typing, Mutation, Oncogenes, Sex Factors, Transcriptome, Cancer Genome Atlas Research Network, General Science & Technology
Abstract

Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis.

Published
2014

45. Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci.

Author

Service, Susan K, Teslovich, Tanya M, Fuchsberger, Christian, Ramensky, Vasily, Yajnik, Pranav, Koboldt, Daniel C, Larson, David E, Zhang, Qunyuan, Lin, Ling, Welch, Ryan, Ding, Li, McLellan, Michael D, O'Laughlin, Michele, Fronick, Catrina, Fulton, Lucinda L, Magrini, Vincent, Swift, Amy, Elliott, Paul, Jarvelin, Marjo-Riitta, Kaakinen, Marika, McCarthy, Mark I, Peltonen, Leena, Pouta, Anneli, Bonnycastle, Lori L, Collins, Francis S, Narisu, Narisu, Stringham, Heather M, Tuomilehto, Jaakko, Ripatti, Samuli, Fulton, Robert S, Sabatti, Chiara, Wilson, Richard K, Boehnke, Michael, and Freimer, Nelson B

Subjects
Humans, Cholesterol, Genotype, Linkage Disequilibrium, Phenotype, Quantitative Trait Loci, Population Groups, European Continental Ancestry Group, Finland, Cholesterol, HDL, Genome-Wide Association Study, High-Throughput Nucleotide Sequencing, HDL, Genetics, Developmental Biology
Abstract

Genome-wide association studies (GWAS) have identified >500 common variants associated with quantitative metabolic traits, but in aggregate such variants explain at most 20-30% of the heritable component of population variation in these traits. To further investigate the impact of genotypic variation on metabolic traits, we conducted re-sequencing studies in >6,000 members of a Finnish population cohort (The Northern Finland Birth Cohort of 1966 [NFBC]) and a type 2 diabetes case-control sample (The Finland-United States Investigation of NIDDM Genetics [FUSION] study). By sequencing the coding sequence and 5' and 3' untranslated regions of 78 genes at 17 GWAS loci associated with one or more of six metabolic traits (serum levels of fasting HDL-C, LDL-C, total cholesterol, triglycerides, plasma glucose, and insulin), and conducting both single-variant and gene-level association tests, we obtained a more complete understanding of phenotype-genotype associations at eight of these loci. At all eight of these loci, the identification of new associations provides significant evidence for multiple genetic signals to one or more phenotypes, and at two loci, in the genes ABCA1 and CETP, we found significant gene-level evidence of association to non-synonymous variants with MAF

Published
2014

46. Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Author

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

Published
2023
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47. Identification of a rare coding variant in complement 3 associated with age-related macular degeneration.

Author

Zhan, Xiaowei, Larson, David, Wang, Chaolong, Koboldt, Daniel, Sergeev, Yuri, Fulton, Robert, Fulton, Lucinda, Fronick, Catrina, Branham, Kari, Bragg-Gresham, Jennifer, Jun, Goo, Hu, Youna, Kang, Hyun, Liu, Dajiang, Othman, Mohammad, Brooks, Matthew, Ratnapriya, Rinki, Boleda, Alexis, Grassmann, Felix, von Strachwitz, Claudia, Olson, Lana, Buitendijk, Gabriëlle, Hofman, Albert, van Duijn, Cornelia, Cipriani, Valentina, Shahid, Humma, Jiang, Yingda, Conley, Yvette, Morgan, Denise, Kim, Ivana, Johnson, Matthew, Cantsilieris, Stuart, Richardson, Andrea, Guymer, Robyn, Luo, Hongrong, Ouyang, Hong, Licht, Christoph, Pluthero, Fred, Zhang, Mindy, Zhang, Kang, Baird, Paul, Blangero, John, Klein, Michael, Farrer, Lindsay, DeAngelis, Margaret, Weeks, Daniel, Yates, John, Klaver, Caroline, Pericak-Vance, Margaret, Haines, Jonathan, Weber, Bernhard, Wilson, Richard, Heckenlively, John, Chew, Emily, Stambolian, Dwight, Mardis, Elaine, Swaroop, Anand, Abecasis, Goncalo, Gorin, Michael, and Moore, Anthony

Subjects
Aging, Complement C3, Complement Factor H, Complement Pathway, Alternative, Gene Frequency, Genetic Variation, Genotype, Macular Degeneration, Polymorphism, Single Nucleotide
Abstract

Macular degeneration is a common cause of blindness in the elderly. To identify rare coding variants associated with a large increase in risk of age-related macular degeneration (AMD), we sequenced 2,335 cases and 789 controls in 10 candidate loci (57 genes). To increase power, we augmented our control set with ancestry-matched exome-sequenced controls. An analysis of coding variation in 2,268 AMD cases and 2,268 ancestry-matched controls identified 2 large-effect rare variants: previously described p.Arg1210Cys encoded in the CFH gene (case frequency (fcase) = 0.51%; control frequency (fcontrol) = 0.02%; odds ratio (OR) = 23.11) and newly identified p.Lys155Gln encoded in the C3 gene (fcase = 1.06%; fcontrol = 0.39%; OR = 2.68). The variants suggest decreased inhibition of C3 by complement factor H, resulting in increased activation of the alternative complement pathway, as a key component of disease biology.

Published
2013

48. Contributors

Author

Ainsworth, Dorothy M., primary, Aleman, Monica, additional, Angelos, John A., additional, Arroyo, Luis G., additional, Austin, Scott M., additional, Axon, Jane E., additional, Ballweber, Lora Rickard, additional, Bannasch, Danika L., additional, Barakzai, Safia Z., additional, Barrell, Emily A., additional, Barrington, George M., additional, Barton, Michelle H., additional, Bauman, Dale E., additional, Beasley, Erin McConachie, additional, Bedenice, Daniela, additional, Benson, Catherine J., additional, Benson, Dionne, additional, Betbeze, Caroline M., additional, Bickett-Weddle, Danelle A., additional, Blikslager, Anthony T., additional, A. Bohn, Andrea, additional, Bordin, Angela I., additional, Bowman, Dwight D., additional, Boyle, Ashley G., additional, Bozorgmanesh, Rana, additional, Bradford, Barry J., additional, Breuhaus, Babetta, additional, Brinsko, Steven P., additional, Browne, Nimet, additional, Buchanan, Ben, additional, Buczinski, Sébastien, additional, Burton, Alexandra J., additional, Burton, Erin N., additional, Byers, Stacey R., additional, Byrne, Barbara A., additional, Byrne, David P., additional, Callan, Robert J., additional, Cargile, Canaan Whitfield, additional, Carlson, Gary P., additional, Carr, Elizabeth A., additional, Carter, Renee T., additional, Casteel, Stan W., additional, Chaffin, M. Keith, additional, Chesen, Berkley, additional, Chigerwe, Munashe, additional, Christensen, Bruce W., additional, Chuck, Gemma, additional, Clothier, Kristin A., additional, Coetzee, Johann (Hans) F., additional, Coleman, Michelle C., additional, Collier, Robert J., additional, Cortese, Victor S., additional, Costa, Lais R., additional, Crossley, Beate M., additional, Davis, Jennifer L., additional, de Laat, Melody Anne, additional, Del Piero, Fabio, additional, Desrochers, André, additional, Dixon, Padraic Martin, additional, Dodd, Charles C., additional, Dominguez, Brandon J., additional, Dore, Vincent, additional, Duhamel, Gerald E., additional, Dunkel, Bettina, additional, Easley, Jack, additional, Ekenstedt, Kari J., additional, Ellis, John A., additional, Espinosa-Mur, Pablo, additional, Erskine, Ronald J., additional, E. Estell, Krista, additional, Evans, Timothy J., additional, Feary, Darien, additional, Fecteau, Gilles, additional, Fecteau, Marie-Eve, additional, Felippe, M. Julia B., additional, Fielding, C. Langdon, additional, Finno, Carrie J., additional, Fleming, Sherrill A., additional, Francoz, David, additional, Frank, Nicholas, additional, Fulton, Robert W., additional, Fultz, Lisa E., additional, Garland, Tam, additional, Garry, Franklyn, additional, Gemensky-Metzler, Anne J., additional, Gibbons, Philippa, additional, Giguère, Steeve, additional, Godden, Sandra, additional, Goff, Jesse Paul, additional, Gonda, Kathleen Casey, additional, Gonzalez, Liara M., additional, Grissett, Gretchen P., additional, Gunn, Alison A., additional, Gutierrez-Nibeyro, Santiago D., additional, Habasha, Faisal Ghazi, additional, Hall, Tiffany L., additional, Halland, Spring K., additional, Hallowell, Gayle D., additional, Hardy, Joanne, additional, Hart, Kelsey A., additional, Hartnack, Amanda K., additional, Heinrich, Daniel A., additional, Heller, Meera, additional, Herthel, Troy, additional, Hietala, Sharon K., additional, Hinchcliff, Kenneth W., additional, Hines, Melissa T., additional, House, John K., additional, Hovda, Lynn R., additional, Hughes, Angela M., additional, Hullinger, Pamela J., additional, Hund, Alexandra, additional, Hurley, David J., additional, James, Robert E., additional, John, Emily, additional, Johns, Jennifer L., additional, Johnson, Philip J., additional, Jones, Meredyth L., additional, Jones, Samuel L., additional, Jordan, Will C., additional, Judy, Carter E., additional, Katzman, Scott A., additional, Klein, Claudia, additional, Kreuder, Amanda J., additional, Lakritz, Jeffrey, additional, Landers, Benjamin, additional, Landolt, Gabriele A., additional, Lascola, Kara M., additional, Lassaline, Mary Elizabeth, additional, LeCouteur, Richard Andrew, additional, Lester, Guy D., additional, Leutenegger, Christian M., additional, Linton, Michelle, additional, Lofstedt, Jeanne, additional, Loinaz, Ricardo, additional, MacKay, Evelyn, additional, MacKay, Robert J., additional, Maclachlan, N. James, additional, Madigan, John E., additional, Magdesian, K. Gary, additional, Makhdoomi, Muhammad Muzafar, additional, Malone, John B., additional, Marsh, Peggy S., additional, Marshall, John F., additional, Martin, Krysta, additional, Mayo, Christie E., additional, Mazan, Melissa, additional, McArt, Jessica A., additional, McConnel, Craig, additional, McDowell, Karen, additional, McFarlane, Dianne, additional, McGill, Jodi L., additional, McGowan, Cathy, additional, McGuirk, Sheila M., additional, McNabb, Bret R., additional, Middleton, John R., additional, Millman, Suzanne T., additional, Morley, Paul S., additional, Mosier, Derek A., additional, Mostrom, Michelle, additional, Nagaraja, T.G., additional, Nichols, Sylvain, additional, Nielsen, Martin K., additional, Norman, Tracy E., additional, Norris, Jeffrey W., additional, Nydam, Daryl, additional, Oliver-Espinosa, Olimpo, additional, Parish, Steven M., additional, Pascoe, John R., additional, Payne, Michael, additional, Plummer, Caryn E., additional, Plummer, Paul J., additional, Poppenga, Robert H., additional, Pratt-Philips, Shannon E., additional, Puschner, Birgit, additional, Pusterla, Nicola, additional, Reef, Virginia B., additional, Renter, David G., additional, Reuss, Sarah M., additional, Reynolds, James P., additional, Romano, Sr., Juan E., additional, Ruegg, Pamela L., additional, Sager, Robert Bascom, additional, Sampson, Sarah N., additional, Sanchez, Chris, additional, Saulez, Montague N., additional, Schott, Harold C., additional, Sharkey, Leslie C., additional, Shearer, Jan K., additional, Slack, JoAnn, additional, Smith, Bradford P., additional, Smith, Geoffrey W., additional, Smith, Rachael L., additional, Spier, Sharon Jane, additional, Sponseller, Brett A., additional, Stämpfli, Henry, additional, St. Jean, Guy, additional, Stewart, Allison Jean, additional, Sweeney, Raymond W., additional, Swor, Tamara M., additional, Taylor, Jared D., additional, Tell, Lisa A., additional, Tennent-Brown, Brett, additional, Terra, Ronald L., additional, Théon, Alain P., additional, Tomlinson, Joy E., additional, Toribio, Ramiro E., additional, Troedsson, Mats H.T., additional, Tull, Travis M., additional, Uzal, Francisco A., additional, Valberg, Stephanie J., additional, Van Amstel, Sarel R., additional, Van Eps, Andrew W., additional, Van Metre, David C., additional, Varner, Dickson D., additional, Voyles, Meredith L., additional, Vygantas, Kristina R., additional, Walz, Paul, additional, Washburn, Kevin, additional, Waters, W. Ray, additional, Watkins, Jeffrey P., additional, Watson, Johanna L., additional, Watts, Ashlee E., additional, Weese, J. Scott, additional, White, Maurice Edward, additional, White, Stephen D., additional, Wilkins, Pamela A., additional, Williams, Jarred, additional, Williams, Kurt J., additional, Wilson, W. David, additional, Woodward, Elizabeth M., additional, Woolums, Amelia R., additional, and Wotman, Kathryn L., additional

Published
2020
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49. Use of Biologics in the Prevention of Infectious Diseases

Author

Pusterla, Nicola, primary, Plummer, Paul J., additional, Cortese, Victor S., additional, Wilson, W. David, additional, Kreuder, Amanda J., additional, Duhamel, Gerald E., additional, Ellis, John A., additional, Fulton, Robert W., additional, Uzal, Francisco A., additional, Taylor, Jared D., additional, and Mosier, Derek A., additional

Published
2020
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50. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Author

Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, onathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Jr., Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Ricketts, Christopher J., De Cubas, Aguirre A., Smith, Christof C., Lang, Martin, Gibb, Ewan A., Bottaro, Donald P., Choueiri, Toni K., Haake, Scott, Hakimi, A. Ari, Henske, Elizabeth P., Hsieh, James J., Ho, Thai H., Krishnan, Bhavani, Kwiatkowski, David J., Merino, Maria J., Nickerson, Michael L., Reuter, Victor E., Shelley, C. Simon, Shuch, Brian, Srinivasan, Ramaprasad, Vincent, Benjamin G., Yang, Lixing, Kim, William Y., and Spellman, Paul T.

Published
2018
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