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51. The Genomic Landscape of Childhood Acute Lymphoblastic Leukemia

Author

Roberts, Kathryn G., primary, Brady, Samuel W., primary, Gu, Zhaohui, primary, Shi, Lei, primary, Pounds, Stanley, primary, Pei, Deqing, primary, Cheng, Cheng, primary, Dai, Yunfeng, primary, Devidas, Meenakshi, primary, Qu, Chunxu, primary, Hill, Ashley, primary, Ma, Xiaotu, primary, Wei, Lei, primary, Arunachalam, Sasi, primary, Hagiwara, Kohei, primary, Liu, Yangling, primary, Flasch, Diane, primary, Liu, Yu, primary, Parker, Matthew, primary, Chen, Xiaolong, primary, Li, Yongjin, primary, Fan, Yiping, primary, Michael, Robert, primary, Rusch, Michael, primary, Wilkinson, Mark, primary, Foy, Scott, primary, Hedges, Dale, primary, Newman, Scott, primary, Zhou, Xin, primary, Wang, Jian, primary, Reshmi, Shalini C., primary, Gastier-Foster, Julie M., primary, Gesuwan, Patee, primary, Smith, Malcolm A, primary, Gerhard, Daniela S., primary, Winick, Naomi, primary, Carroll, Andrew J., primary, Heerema, Nyla A., primary, Harvey, Richard C., primary, Willman, Cheryl L., primary, Larsen, Eric, primary, Raetz, Elizabeth A., primary, Borowitz, Michael J., primary, Wood, Brent L, primary, Carroll, William L., primary, Zweidler-McKay, Patrick A., primary, Rabin, Karen R., primary, Mattano, Leonard A., primary, Maloney, Kelly, primary, Winter, Stuart S., primary, Burke, Michael J., primary, Salzer, Wanda L., primary, Dunsmore, Kimberly P., primary, Angiolillo, Anne, primary, Crews, Kristine R, primary, Downing, James R., primary, Jeha, Sima, primary, Evans, William E., primary, Pui, Ching-Hon, primary, Yang, Jun J., primary, Relling, Mary V., primary, Hunger, Stephen P., primary, Loh, Mignon L., primary, Zhang, Jinghui, primary, and Mullighan, Charles G., primary

Published
2019
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52. Comprehensive molecular characterization of pediatric treatment-induced high-grade glioma: A distinct entity despite disparate etiologies with defining molecular characteristics and potential therapeutic targets

Author

DeSisto, John, primary, Lucas, John T., additional, Xu, Ke, additional, Donson, Andrew, additional, Lin, Tong, additional, Sanford, Bridget, additional, Wu, Gang, additional, Tran, Quynh T., additional, Hedges, Dale, additional, Hsu, Chih-Yang, additional, Armstrong, Gregory T., additional, Arnold, Michael, additional, Bhatia, Smita, additional, Flannery, Patrick, additional, Lemma, Rakeb, additional, Hardie, Lakotah, additional, Schüller, Ulrich, additional, Hoffman, Lindsey M., additional, Dorris, Kathleen, additional, Levy, Jean Mulcahy, additional, Hankinson, Todd C., additional, Handler, Michael, additional, Liu, Arthur, additional, Foreman, Nicholas, additional, Vibhakar, Rajeev, additional, Jones, Kenneth, additional, Allen, Sariah, additional, Zhang, Jinghui, additional, Baker, Suzanne J., additional, Merchant, Thomas E., additional, Orr, Brent A., additional, and Green, Adam L., additional

Published
2019
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53. Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants

Author

Edmonson, Michael N., primary, Patel, Aman N., additional, Hedges, Dale J., additional, Wang, Zhaoming, additional, Rampersaud, Evadnie, additional, Kesserwan, Chimene A., additional, Zhou, Xin, additional, Liu, Yanling, additional, Newman, Scott, additional, Rusch, Michael C., additional, McLeod, Clay L., additional, Wilkinson, Mark R., additional, Rice, Stephen V., additional, Soussi, Thierry, additional, Taylor, J. Paul, additional, Benatar, Michael, additional, Becksfort, Jared B., additional, Nichols, Kim E., additional, Robison, Leslie L., additional, Downing, James R., additional, and Zhang, Jinghui, additional

Published
2019
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54. An X chromosome-wide association study in autism families identifies TBL1X as a novel autism spectrum disorder candidate gene in males

Author

Chung Ren-Hua, Ma Deqiong, Wang Kai, Hedges Dale J, Jaworski James M, Gilbert John R, Cuccaro Michael L, Wright Harry H, Abramson Ruth K, Konidari Ioanna, Whitehead Patrice L, Schellenberg Gerard D, Hakonarson Hakon, Haines Jonathan L, Pericak-Vance Margaret A, and Martin Eden R

Subjects
Neurology. Diseases of the nervous system, RC346-429
Abstract

Abstract Background Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with a strong genetic component. The skewed prevalence toward males and evidence suggestive of linkage to the X chromosome in some studies suggest the presence of X-linked susceptibility genes in people with ASD. Methods We analyzed genome-wide association study (GWAS) data on the X chromosome in three independent autism GWAS data sets: two family data sets and one case-control data set. We performed meta- and joint analyses on the combined family and case-control data sets. In addition to the meta- and joint analyses, we performed replication analysis by using the two family data sets as a discovery data set and the case-control data set as a validation data set. Results One SNP, rs17321050, in the transducin β-like 1X-linked (TBL1X) gene [OMIM:300196] showed chromosome-wide significance in the meta-analysis (P value = 4.86 × 10-6) and joint analysis (P value = 4.53 × 10-6) in males. The SNP was also close to the replication threshold of 0.0025 in the discovery data set (P = 5.89 × 10-3) and passed the replication threshold in the validation data set (P = 2.56 × 10-4). Two other SNPs in the same gene in linkage disequilibrium with rs17321050 also showed significance close to the chromosome-wide threshold in the meta-analysis. Conclusions TBL1X is in the Wnt signaling pathway, which has previously been implicated as having a role in autism. Deletions in the Xp22.2 to Xp22.3 region containing TBL1X and surrounding genes are associated with several genetic syndromes that include intellectual disability and autistic features. Our results, based on meta-analysis, joint analysis and replication analysis, suggest that TBL1X may play a role in ASD risk.

Published
2011
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55. Alu repeats increase local recombination rates

Author

Hedges Dale J, Tolpinrud Whitney L, Xing Jinchuan, Zhang Yuhua, Watkins W Scott, Witherspoon David J, Batzer Mark A, and Jorde Lynn B

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Recombination rates vary widely across the human genome, but little of that variation is correlated with known DNA sequence features. The genome contains more than one million Alu mobile element insertions, and these insertions have been implicated in non-homologous recombination, modulation of DNA methylation, and transcriptional regulation. If individual Alu insertions have even modest effects on local recombination rates, they could collectively have a significant impact on the pattern of linkage disequilibrium in the human genome and on the evolution of the Alu family itself. Results We carried out sequencing, SNP identification, and SNP genotyping around 19 AluY insertion loci in 347 individuals sampled from diverse populations, then used the SNP genotypes to estimate local recombination rates around the AluY loci. The loci and SNPs were chosen so as to minimize other factors (such as SNP ascertainment bias and SNP density) that could influence recombination rate estimates. We detected a significant increase in recombination rate within ~2 kb of the AluY insertions in our African population sample. To test this observation against a larger set of AluY insertions, we applied our locus- and SNP-selection design and analyses to the HapMap Phase II data. In that data set, we observed a significantly increased recombination rate near AluY insertions in both the CEU and YRI populations. Conclusion We show that the presence of a fixed AluY insertion is significantly predictive of an elevated local recombination rate within 2 kb of the insertion, independent of other known predictors. The magnitude of this effect, approximately a 6% increase, is comparable to the effects of some recombinogenic DNA sequence motifs identified via their association with recombination hot spots.

Published
2009
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56. Analysis of the human Alu Ye lineage

Author

Jurka Jerzy, Hedges Dale J, Ray David A, Salem Abdel-Halim, and Batzer Mark A

Subjects
Evolution, QH359-425
Abstract

Abstract Background Alu elements are short (~300 bp) interspersed elements that amplify in primate genomes through a process termed retroposition. The expansion of these elements has had a significant impact on the structure and function of primate genomes. Approximately 10 % of the mass of the human genome is comprised of Alu elements, making them the most abundant short interspersed element (SINE) in our genome. The majority of Alu amplification occurred early in primate evolution, and the current rate of Alu retroposition is at least 100 fold slower than the peak of amplification that occurred 30–50 million years ago. Alu elements are therefore a rich source of inter- and intra-species primate genomic variation. Results A total of 153 Alu elements from the Ye subfamily were extracted from the draft sequence of the human genome. Analysis of these elements resulted in the discovery of two new Alu subfamilies, Ye4 and Ye6, complementing the previously described Ye5 subfamily. DNA sequence analysis of each of the Alu Ye subfamilies yielded average age estimates of ~14, ~13 and ~9.5 million years old for the Alu Ye4, Ye5 and Ye6 subfamilies, respectively. In addition, 120 Alu Ye4, Ye5 and Ye6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and levels of human genomic diversity. Conclusion The Alu Ye lineage appears to have started amplifying relatively early in primate evolution and continued propagating at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Detailed sequence analysis of several Alu pre-integration sites indicated that multiple types of events had occurred, including gene conversions, near-parallel independent insertions of different Alu elements and Alu-mediated genomic deletions. A potential hotspot for Alu insertion in the Fer1L3 gene on chromosome 10 was also identified.

Published
2005
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57. Integrating somatic variant data and biomarkers for germline variant classification in cancer predisposition genes

Author

Walsh, Michael F., primary, Ritter, Deborah I., additional, Kesserwan, Chimene, additional, Sonkin, Dmitriy, additional, Chakravarty, Debyani, additional, Chao, Elizabeth, additional, Ghosh, Rajarshi, additional, Kemel, Yelena, additional, Wu, Gang, additional, Lee, Kristy, additional, Kulkarni, Shashikant, additional, Hedges, Dale, additional, Mandelker, Diana, additional, Ceyhan‐Birsoy, Ozge, additional, Luo, Minjie, additional, Drazer, Michael, additional, Zhang, Liying, additional, Offit, Kenneth, additional, and Plon, Sharon E., additional

Published
2018
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58. Genetic Risk for Subsequent Neoplasms Among Long-Term Survivors of Childhood Cancer

Author

Wang, Zhaoming, primary, Wilson, Carmen L., additional, Easton, John, additional, Thrasher, Andrew, additional, Mulder, Heather, additional, Liu, Qi, additional, Hedges, Dale J., additional, Wang, Shuoguo, additional, Rusch, Michael C., additional, Edmonson, Michael N., additional, Levy, Shawn, additional, Lanctot, Jennifer Q., additional, Caron, Eric, additional, Shelton, Kyla, additional, Currie, Kelsey, additional, Lear, Matthew, additional, Patel, Aman, additional, Rosencrance, Celeste, additional, Shao, Ying, additional, Vadodaria, Bhavin, additional, Yergeau, Donald, additional, Sapkota, Yadav, additional, Brooke, Russell J., additional, Moon, Wonjong, additional, Rampersaud, Evadnie, additional, Ma, Xiaotu, additional, Chang, Ti-Cheng, additional, Rice, Stephen V., additional, Pepper, Cynthia, additional, Zhou, Xin, additional, Chen, Xiang, additional, Chen, Wenan, additional, Jones, Angela, additional, Boone, Braden, additional, Ehrhardt, Matthew J., additional, Krasin, Matthew J., additional, Howell, Rebecca M., additional, Phillips, Nicholas S., additional, Lewis, Courtney, additional, Srivastava, Deokumar, additional, Pui, Ching-Hon, additional, Kesserwan, Chimene A., additional, Wu, Gang, additional, Nichols, Kim E., additional, Downing, James R., additional, Hudson, Melissa M., additional, Yasui, Yutaka, additional, Robison, Leslie L., additional, and Zhang, Jinghui, additional

Published
2018
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59. Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): A Cloud-based Platform for Curating and Classifying Germline Variants

Author

Edmonson, Michael N., primary, Patel, Aman N., additional, Hedges, Dale J., additional, Wang, Zhaoming, additional, Rampersaud, Evadnie, additional, Kesserwan, Chimene A., additional, Zhou, Xin, additional, Liu, Yanling, additional, Newman, Scott, additional, Rusch, Michael C., additional, McLeod, Clay L., additional, Wilkinson, Mark R., additional, Rice, Stephen V., additional, Becksfort, Jared B., additional, Nichols, Kim E., additional, Robison, Leslie L., additional, Downing, James R., additional, and Zhang, Jinghui, additional

Published
2018
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60. Abstract 3001: Germline mutations in cancer predisposition genes and risk for subsequent neoplasms among long-term survivors of childhood cancer in the St. Jude Lifetime Cohort

Author

Wang, Zhaoming, primary, Wilson, Carmen L., additional, Easton, John, additional, Hedges, Dale, additional, Liu, Qi, additional, Wu, Gang, additional, Rusch, Michael, additional, Edmonson, Michael, additional, Levy, Shawn, additional, Lanctot, Jennifer Q., additional, Caron, Eric, additional, Shelton, Kyla, additional, Currie, Kelsey, additional, Lear, Matthew, additional, Mulder, Heather L., additional, Yergeau, Donald, additional, Rosencrance, Celeste, additional, Vadodaria, Bhavin, additional, Sapkota, Yadav, additional, Brooke, Russell J., additional, Moon, Wonjong, additional, Rampersaud, Evadnie, additional, Ma, Xiaotu, additional, Wang, Shuoguo, additional, Chang, Ti-Cheng, additional, Rice, Stephen, additional, Thrasher, Andrew, additional, Patel, Aman, additional, Pepper, Cynthia, additional, Zhou, Xin, additional, Chen, Xiang, additional, Chen, Wenan, additional, Jones, Angela, additional, Boone, Braden, additional, Srivastava, Deo Kumar, additional, Kesserwan, Chimene A., additional, Nichols, Kim E., additional, Downing, James R., additional, Hudson, Melissa M., additional, Yasui, Yutaka, additional, Robison, Leslie L., additional, and Zhang, Jinghui, additional

Published
2017
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61. Lipoblastomas presenting in older children and adults: analysis of 22 cases with identification of novel PLAG1fusion partners

Author

Fritchie, Karen, Wang, Lu, Yin, Zhaohong, Nakitandwe, Joy, Hedges, Dale, Horvai, Andrew, Mora, Jorge Torres, Folpe, Andrew L., and Bahrami, Armita

Abstract

Lipoblastomas are benign neoplasms of embryonal white fat that typically present in the first 3 years of life and show a lobular arrangement of maturing adipocytes with variable degrees of myxoid change. We systematically studied the clinicopathologic and genetic features of lipoblastomas arising in older children and adults. Cases with a diagnosis of lipoblastoma or maturing lipoblastoma in patients >3 years of age were retrieved from our archives. Immunostaining for CD34 and desmin and molecular studies (FISH, RNA sequencing) were performed. Twenty-two cases (8F; 14M) were identified in patients ranging from 4 to 44 years of age (median 10 years). Sites included extremity (n?=?15), head and neck (n?=?4), and trunk (n?=?3) with tumor sizes varying from 1.6 to 17.5?cm (median 5). Only three tumors had histologic features of “conventional” lipoblastoma. The majority of tumors (n?=?14) were composed of variably sized lobules of mature adipose tissue partitioned by thin fibrous septa (“maturing”). The remaining five cases consisted predominantly of bland spindled to plump ovoid cells embedded in a fibrous stroma, with a vaguely plexiform arrangement of small myxoid and adipocytic nodules (“fibroblastic”). CD34 was diffusely positive in all cases tested (21/21), while desmin immunoreactivity was identified in 12 of 21 cases (diffuse?=?7, focal?=?5). PLAG1rearrangements were identified in 13 tumors in the entire cohort (59%), including all 5 fibroblastic tumors. RNA sequencing detected eight PLAG1fusion partners, of which two were known (CHCHD7and COL3A1) and six were novel (SRSF3, HNRNPC, PCMTD1, YWHAZ, CTDSP2, and PPP2R2A). Twelve cases had follow-up (1–107 months; median 21 months), and no recurrences were reported. Lipoblastomas may occur in older children and adults and may be difficult to recognize due to their predominantly adipocytic or fibrous appearance. Awareness that lipoblastomas may occur in older patients, careful evaluation for foci showing more typical morphologic features, ancillary immunohistochemistry for CD34 and desmin, and molecular genetic studies to identify PLAG1rearrangements are the keys to recognizing these tumors.

Published
2021
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63. Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health

Author

Belancio, Victoria P., Hedges, Dale J., and Deininger, Prescott

Subjects
Mammals -- Genetic aspects, Retrotransposons -- Genetic aspects, Retrotransposons -- Research, Transposons -- Research, Transposons -- Health aspects, Eukaryotes, Health
Abstract

The study investigates elements of non-long-terminal-repeat (non-LTR) mammalian retrotransposon biology, focusing on human retrotransposon activity. Their potential effect on host biology and the connotations for the nature of transposable element-host association is also examined.

Published
2008

64. A comprehensive approach to expression of L1 loci

Author

Deininger, Prescott, primary, Morales, Maria E., additional, White, Travis B., additional, Baddoo, Melody, additional, Hedges, Dale J., additional, Servant, Geraldine, additional, Srivastav, Sudesh, additional, Smither, Madison E., additional, Concha, Monica, additional, DeHaro, Dawn L., additional, Flemington, Erik K., additional, and Belancio, Victoria P., additional

Published
2016
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65. Under the genomic radar: The stealth model of Alu amplification

Author

Kyudong Han, Jinchuan Xing, Hui Wang, Hedges, Dale J., Garber, Randall K., Batzer, Mark A., and Cordaux, Richard

Subjects
Computational biology -- Analysis, Human genome -- Analysis, Arithmetic logic unit, Computer arithmetic and logic units, Health
Abstract

The evolutionary history of the AluYb lineage, one of the most active Alu lineages in the human genome is restructured using both computational and wet-bench approaches. A demonstration that the major AluYb lineage expansion in humans is a species-specific event, as nonhuman primates posses only a handful o AluYb elements is discussed.

Published
2005

66. Differential Alu mobilization and polymorphism among the human and chimpanzee lineages

Author

Hedges, Dale J., Callinan, Pauline A., Cordaux, Richard, Xing, Jinchuan, Barnes, Erin, and Batzer, Mark A.

Subjects
Human genetics -- Research, Genetic polymorphisms -- Research, Chimpanzees -- Genetic aspects, Health
Abstract

Chromosomal-level comparison between the Alu retroposition dynamics consisting of the differential Alu mobilization and polymorphism dynamics, which has occurred after the divergence of human and the chimpanzees is analyzed. Comparison in the Alu insertions of humans and the chimpanzees has shown a two-fold increase in the Alu insertions of the humans.

Published
2004

67. Active Alu element 'A-tails': size does matter

Author

Roy-Engel, Astrid M., Salem, Abdel-Halim, Oyeniran, Oluwatosin O., Deininger, Lisa, Hedges, Dale J., Kilroy, Gail E., Batzer, Mark A., and Deininger, Prescott L.

Subjects
Nucleotide sequence -- Analysis, Genes -- Analysis, Genomes -- Analysis, Human chromosomes -- Analysis, Health
Abstract

Results indicate that the length of the Alu 'A-tails', belonging to interspersed SINE elements family, is one of the main factors determining the retropositional capability of an Alu element. Data reveal that Alu elements exhibit tails of 40 or more adenosine residues and the A streches of the Alu subfamilies vary. Furthermore, the A-tail length determines which Alu elements are active.

Published
2002

68. An Improved Workflow for miRNA Expression Profiling Using Ion Semiconductor Sequencing

Author

Clarke, Jennifer, Andersen, Ashley, Navarro, Loida, Cardentey, Yoslayma, Hulme, William, Bademci, Guney, van Booven, Derek, Hedges, Dale, Pericak-Vance, Margaret, Gilbert, John, and Guettouche, Toumy

Subjects
Scientific Poster Abstracts
Abstract

MicroRNAs (miRNAs) are non coding RNA molecules with a size range of 18 to 24 nucleotides that have important functions in regulating numerous cellular processes. Several technologies such as microarrays, real-time PCR and second-generation deep sequencing have been used to profile miRNA expression and characterize variances in miRNA species. This study focuses on miRNA expression profiling using ion semiconductor sequencing with an improved workflow that utilizes multi-channel microfluidics to isolate miRNAs from total RNA. This microfluidics approach replaces polyacrylamide gel electrophoresis for size fractionation and enrichment of miRNAs commonly used in sequencing protocols. We compared miRNA expression profiles of commercially available preparations of lung and brain total RNA obtained by ion semiconductor sequencing, second-generation sequencing and real-time PCR array. We show that ion semiconductor sequencing using our improved workflow with the microfluidics device produced similar miRNA expression profiles compared to polyacrylamide gel based methods. We also detected similar numbers of miRNAs compared to second-generation deep sequencing. Finally, we were able to validate our results using a commercially available real-time PCR based miRNA array. Our workflow streamlines and significantly improves the utilization of semiconductor sequencing for miRNA profiling both in a research and clinical environment.

Published
2012

72. A Genomic Search for Alzheimer's Disease Genes

Author

Haines, Jonathan L., primary, Bailey, L. Renee, additional, Grubber, Janet M., additional, Hedges, Dale, additional, Hall, Jenifer L., additional, West, Sandra, additional, Santoro, Leonard, additional, Kemmerer, Beth, additional, Saunders, Anne M., additional, Roses, Allen D., additional, Small, Gary W., additional, Scott, William K., additional, Conneally, P. Michael, additional, Vance, Jeffery M., additional, and Pericak-Vance, Margaret A., additional

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74. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Author

Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., Hunter, Wayne, Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., and Hunter, Wayne

Abstract

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

Published
2010
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75. Genetic heterogeneity between paired primary and metastatic solid tumors and implications for neoantigen-based personalized cancer vaccines.

Author

Shaw, Timothy I, Chang, Darwin, Obermayer, Alyssa N, Hedges, Dale, Tan, Aik-choon, Naqash, Abdul Rafeh, Gatti-Mays, Margaret Elena, Ratan, Aakrosh, McCarter, Martin, Carpten, John D., Colman, Howard, Puzanov, Igor, Arnold, Susanne M., Churchman, Michelle L., Hwu, Patrick, Dalton, William S., Weiner, George J., Conejo-Garcia, Jose, Rodriguez, Paulo, and Tarhini, Ahmad A.

Published
2023
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77. Reconstructing the Population Genetic History of the Caribbean

Author

Moreno-Estrada, Andrés, primary, Gravel, Simon, additional, Zakharia, Fouad, additional, McCauley, Jacob L., additional, Byrnes, Jake K., additional, Gignoux, Christopher R., additional, Ortiz-Tello, Patricia A., additional, Martínez, Ricardo J., additional, Hedges, Dale J., additional, Morris, Richard W., additional, Eng, Celeste, additional, Sandoval, Karla, additional, Acevedo-Acevedo, Suehelay, additional, Norman, Paul J., additional, Layrisse, Zulay, additional, Parham, Peter, additional, Martínez-Cruzado, Juan Carlos, additional, Burchard, Esteban González, additional, Cuccaro, Michael L., additional, Martin, Eden R., additional, and Bustamante, Carlos D., additional

Published
2013
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79. Exome Sequencing and Genome-Wide Linkage Analysis in 17 Families Illustrate the Complex Contribution of TTN Truncating Variants to Dilated Cardiomyopathy

Author

Norton, Nadine, primary, Li, Duanxiang, additional, Rampersaud, Evadnie, additional, Morales, Ana, additional, Martin, Eden R., additional, Zuchner, Stephan, additional, Guo, Shengru, additional, Gonzalez, Michael, additional, Hedges, Dale J., additional, Robertson, Peggy D., additional, Krumm, Niklas, additional, Nickerson, Deborah A., additional, and Hershberger, Ray E., additional

Published
2013
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80. A comprehensive approach to expression of L1 loci.

Author

Deininger, Prescott, Morales, Maria E., White, Travis B., Baddoo, Melody, Hedges, Dale J., Servant, Geraldine, Srivastav, Sudesh, Smither, Madison E., Concha, Monica, DeHaro, Dawn L., Flemington, Erik K., and Belancio, Victoria P.

Published
2017
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81. Whole-Exome Sequencing in Multiplex Families Identifies Novel Rare Variants in Multiple Sclerosis (P05.137)

Author

Haines, Jonathan, primary, Beecham, Ashley, additional, McCauley, Jacob, additional, Hadjixenofontos, Athena, additional, Whitehead, Patrice, additional, Konidari, Ioanna, additional, Aviram, Anat, additional, Pasco, Yuslin, additional, Hauser, Stephen, additional, Oksenberg, Jorge, additional, Hedges, Dale, additional, Vance, Jeffery, additional, and Pericak-Vance, Margaret, additional

Published
2013
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82. Whole-Genome Sequencing of the Akata and Mutu Epstein-Barr Virus Strains

Author

Lin, Zhen, primary, Wang, Xia, additional, Strong, Michael J., additional, Concha, Monica, additional, Baddoo, Melody, additional, Xu, Guorong, additional, Baribault, Carl, additional, Fewell, Claire, additional, Hulme, William, additional, Hedges, Dale, additional, Taylor, Christopher M., additional, and Flemington, Erik K., additional

Published
2013
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83. Evaluating Mitochondrial DNA Variation in Autism Spectrum Disorders

Author

Hadjixenofontos, Athena, primary, Schmidt, Michael A., additional, Whitehead, Patrice L., additional, Konidari, Ioanna, additional, Hedges, Dale J., additional, Wright, Harry H., additional, Abramson, Ruth K., additional, Menon, Ramkumar, additional, Williams, Scott M., additional, Cuccaro, Michael L., additional, Haines, Jonathan L., additional, Gilbert, John R., additional, Pericak-Vance, Margaret A., additional, Martin, Eden R., additional, and McCauley, Jacob L., additional

Published
2012
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86. Whole-Exome Sequencing Identifies Novel Risk Variant for Thrombotic Storm

Author

Ortel, Thomas L., primary, Beecham, Gary, additional, Hedges, Dale, additional, Whitehead, Patrice, additional, Beecham, Ashley, additional, Hahn, Susan, additional, Lawson, Janice W., additional, Erkan, Doruk, additional, Brandao, Leonardo R., additional, James, Andra H., additional, Manco-Johnson, Marilyn J., additional, Kulkarni, Roshni, additional, Kitchens, Craig S., additional, Pericak-Vance, Margaret, additional, and Vance, Jeffery M, additional

Published
2011
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87. Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform

Author

Hedges, Dale J., primary, Guettouche, Toumy, additional, Yang, Shan, additional, Bademci, Guney, additional, Diaz, Ashley, additional, Andersen, Ashley, additional, Hulme, William F., additional, Linker, Sara, additional, Mehta, Arpit, additional, Edwards, Yvonne J. K., additional, Beecham, Gary W., additional, Martin, Eden R., additional, Pericak-Vance, Margaret A., additional, Zuchner, Stephan, additional, Vance, Jeffery M., additional, and Gilbert, John R., additional

Published
2011
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88. Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq

Author

Xu, Guorong, primary, Fewell, Claire, additional, Taylor, Christopher, additional, Deng, Nan, additional, Hedges, Dale, additional, Wang, Xia, additional, Zhang, Kun, additional, Lacey, Michelle, additional, Zhang, Haitao, additional, Yin, Qinyan, additional, Cameron, Jennifer, additional, Lin, Zhen, additional, Zhu, Dongxiao, additional, and Flemington, Erik K., additional

Published
2010
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89. Readers Report.

Author

Caswell, J. B., Kantor, Mark, Lang, Mark, Angert, Stuart H., Scott, Angela P., Hedges, Dale, von Hippel, Arndt, Barbaro, Pete, Deal, Timothy E., and Fricklas, Michael D.

Subjects
LETTERS to the editor, ACCOUNTING changes, INVESTORS, PETROLEUM product sales & prices, INDUSTRIAL laws & legislation
Abstract

Several letters to the editor are presented in response to articles in previous issues including "Accounting changes that keep investors in dark," by Jennifer Reingold in the February 9, 1998 issue, "How low can oil prices go?," in the February 2, 1998 issue, and "Prying open the open skies," in the February 9, 1998 issue.

Published
1998

90. Correction: Exome Sequencing of a Multigenerational Human Pedigree

Author

Hedges, Dale J., primary, Burges, Dan, additional, Powell, Eric, additional, Almonte, Cherylyn, additional, Huang, Jia, additional, Young, Stuart, additional, Boese, Benjamin, additional, Schmidt, Mike, additional, Pericak-Vance, Margaret A., additional, Martin, Eden, additional, Zhang, Xinmin, additional, Harkins, Timothy T., additional, and Züchner, Stephan, additional

Published
2009
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91. Exome Sequencing of a Multigenerational Human Pedigree

Author

Hedges, Dale, primary, Burges, Dan, additional, Powell, Eric, additional, Almonte, Cherylyn, additional, Huang, Jia, additional, Young, Stuart, additional, Boese, Benjamin, additional, Schmidt, Mike, additional, Pericak-Vance, Margaret A., additional, Martin, Eden, additional, Zhang, Xinmin, additional, Harkins, Timothy T., additional, and Züchner, Stephan, additional

Published
2009
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94. Alu repeats increase local recombination rates

Author

Witherspoon, David J, primary, Watkins, W Scott, additional, Zhang, Yuhua, additional, Xing, Jinchuan, additional, Tolpinrud, Whitney L, additional, Hedges, Dale J, additional, Batzer, Mark A, additional, and Jorde, Lynn B, additional

Published
2009
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