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1. The genomic basis of childhood T-lineage acute lymphoblastic leukaemia

Author

Pölönen, Petri, Di Giacomo, Danika, Seffernick, Anna Eames, Elsayed, Abdelrahman, Kimura, Shunsuke, Benini, Francesca, Montefiori, Lindsey E., Wood, Brent L., Xu, Jason, Chen, Changya, Cheng, Zhongshan, Newman, Haley, Myers, Jason, Iacobucci, Ilaria, Li, Elizabeth, Sussman, Jonathan, Hedges, Dale, Hui, Yawei, Diorio, Caroline, Uppuluri, Lahari, Frank, David, Fan, Yiping, Chang, Yunchao, Meshinchi, Soheil, Ries, Rhonda, Shraim, Rawan, Li, Alexander, Bernt, Kathrin M., Devidas, Meenakshi, Winter, Stuart S., Dunsmore, Kimberly P., Inaba, Hiroto, Carroll, William L., Ramirez, Nilsa C., Phillips, Aaron H., Kriwacki, Richard W., Yang, Jun J., Vincent, Tiffaney L., Zhao, Yaqi, Ghate, Pankaj S., Wang, Jian, Reilly, Colleen, Zhou, Xin, Sanders, Mathijs A., Takita, Junko, Kato, Motohiro, Takasugi, Nao, Chang, Bill H., Press, Richard D., Loh, Mignon, Rampersaud, Evadnie, Raetz, Elizabeth, Hunger, Stephen P., Tan, Kai, Chang, Ti-Cheng, Wu, Gang, Pounds, Stanley B., Mullighan, Charles G., and Teachey, David T.

Published
2024
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3. Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia

Author

Ryan, Sarra L., Peden, John F., Kingsbury, Zoya, Schwab, Claire J., James, Terena, Polonen, Petri, Mijuskovic, Martina, Becq, Jenn, Yim, Richard, Cranston, Ruth E., Hedges, Dale J., Roberts, Kathryn G., Mullighan, Charles G., Vora, Ajay, Russell, Lisa J., Bain, Robert, Moorman, Anthony V., Bentley, David R., Harrison, Christine J., and Ross, Mark T.

Published
2023
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4. Genomic landscape of Down syndrome–associated acute lymphoblastic leukemia

Author

Li, Zhenhua, Chang, Ti-Cheng, Junco, Jacob J., Devidas, Meenakshi, Li, Yizhen, Yang, Wenjian, Huang, Xin, Hedges, Dale J., Cheng, Zhongshan, Shago, Mary, Carroll, Andrew J., Heerema, Nyla A., Gastier-Foster, Julie, Wood, Brent L., Borowitz, Michael J., Sanclemente, Lauren, Raetz, Elizabeth A., Hunger, Stephen P., Feingold, Eleanor, Rosser, Tracie C., Sherman, Stephanie L., Loh, Mignon L., Mullighan, Charles G., Yu, Jiyang, Wu, Gang, Lupo, Philip J., Rabin, Karen R., and Yang, Jun J.

Published
2023
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5. RNA-seq Fusion Detection in Clinical Oncology

Author

Hedges, Dale J., Crusio, Wim E., Series Editor, Dong, Haidong, Series Editor, Radeke, Heinfried H., Series Editor, Rezaei, Nima, Series Editor, Steinlein, Ortrud, Series Editor, Xiao, Junjie, Series Editor, and Laganà, Alessandro, editor

Published
2022
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6. Sequential Approach to Improve the Molecular Classification of Childhood Acute Lymphoblastic Leukemia

Author

Yu, Chih-Hsiang, Wu, Gang, Chang, Chia-Ching, Jou, Shiann-Tarng, Lu, Meng-Yao, Lin, Kai-Hsin, Chen, Shu-Huey, Wu, Kang-Hsi, Huang, Fang-Liang, Cheng, Chao-Neng, Chang, Hsiu-Hao, Hedges, Dale, Wang, Jinn-Li, Yen, Hsiu-Ju, Li, Meng-Ju, Chou, Shu-Wei, Hung, Chen-Ting, Lin, Ze-Shiang, Lin, Chien-Yu, Chen, Hsuan-Yu, Ni, Yu-Ling, Hsu, Yin-Chen, Lin, Dong-Tsamn, Lin, Shu-Wha, Yang, Jun J., Pui, Ching-Hon, Yu, Sung-Liang, and Yang, Yung-Li

Published
2022
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7. The genomic landscape of pediatric acute lymphoblastic leukemia

Author

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

Published
2022
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9. Genomic Determinants of Outcome in Acute Lymphoblastic Leukemia.

Author

Chang, Ti-Cheng, Chen, Wenan, Qu, Chunxu, Cheng, Zhongshan, Hedges, Dale, Elsayed, Abdelrahman, Pounds, Stanley B., Shago, Mary, Rabin, Karen R., Raetz, Elizabeth A., Devidas, Meenakshi, Cheng, Cheng, Angiolillo, Anne, Baviskar, Pradyuamna, Borowitz, Michael, Burke, Michael J., Carroll, Andrew, Carroll, William L., Chen, I-Ming, and Harvey, Richard

Published
2024
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11. Reconstructing the Population Genetic History of the Caribbean

Author

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

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics
Abstract

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by making use of genome-wide SNP array data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean., Comment: 26 pages, 6 figures, and supporting information

Published
2013

12. Comprehensive molecular characterization of pediatric radiation-induced high-grade glioma

Author

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

Published
2021
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14. Evidence of novel fine-scale structural variation at autism spectrum disorder candidate loci

Author

Hedges, Dale J, Hamilton-Nelson, Kara L, Sacharow, Stephanie J, Nations, Laura, Beecham, Gary W, Kozhekbaeva, Zhanna M, Butler, Brittany L, Cukier, Holly N, Whitehead, Patrice L, Ma, Deqiong, Jaworski, James M, Nathanson, Lubov, Lee, Joycelyn M, Hauser, Stephen L, Oksenberg, Jorge R, Cuccaro, Michael L, Haines, Jonathan L, Gilbert, John R, and Pericak-Vance, Margaret A

Abstract

Abstract Background Autism spectrum disorders (ASD) represent a group of neurodevelopmental disorders characterized by a core set of social-communicative and behavioral impairments. Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the brain, acting primarily via the GABA receptors (GABR). Multiple lines of evidence, including altered GABA and GABA receptor expression in autistic patients, indicate that the GABAergic system may be involved in the etiology of autism. Methods As copy number variations (CNVs), particularly rare and de novo CNVs, have now been implicated in ASD risk, we examined the GABA receptors and genes in related pathways for structural variation that may be associated with autism. We further extended our candidate gene set to include 19 genes and regions that had either been directly implicated in the autism literature or were directly related (via function or ancestry) to these primary candidates. For the high resolution CNV screen we employed custom-designed 244 k comparative genomic hybridization (CGH) arrays. Collectively, our probes spanned a total of 11 Mb of GABA-related and additional candidate regions with a density of approximately one probe every 200 nucleotides, allowing a theoretical resolution for detection of CNVs of approximately 1 kb or greater on average. One hundred and sixty-eight autism cases and 149 control individuals were screened for structural variants. Prioritized CNV events were confirmed using quantitative PCR, and confirmed loci were evaluated on an additional set of 170 cases and 170 control individuals that were not included in the original discovery set. Loci that remained interesting were subsequently screened via quantitative PCR on an additional set of 755 cases and 1,809 unaffected family members. Results Results include rare deletions in autistic individuals at JAKMIP1, NRXN1, Neuroligin4Y, OXTR, and ABAT. Common insertion/deletion polymorphisms were detected at several loci, including GABBR2 and NRXN3. Overall, statistically significant enrichment in affected vs. unaffected individuals was observed for NRXN1 deletions. Conclusions These results provide additional support for the role of rare structural variation in ASD.

Published
2012

15. The genomic basis of childhood T-lineage acute lymphoblastic leukemia

Author

Mullighan, Charles, primary, Pölönen, Petri, additional, Giacomo, Danika Di, additional, Seffernick, Anna, additional, Elsayed, Abdelrahman, additional, Kimura, Shunsuke, additional, Benini, Francesca, additional, Montefiori, Lindsey, additional, Wood, Brent, additional, Xu, Jason, additional, Chen, Changya, additional, Cheng, Zhongshan, additional, Newman, Haley, additional, Myers, Jason, additional, Iacobucci, Ilaria, additional, Li, Elizabeth, additional, Sussman, Jonathan, additional, Hedges, Dale, additional, Hui, Yawei, additional, Diorio, Caroline, additional, Uppuluri, Lahari, additional, Frank, David, additional, Fan, Yiping, additional, Chang, Yunchao, additional, Meshinchi, Soheil, additional, Ries, Rhonda, additional, Shraim, Rawan, additional, Li, Alexander, additional, Bernt, Kathrin, additional, Devidas, Meenakshi, additional, Winter, Stuart, additional, Dunsmore, Kimberley, additional, Inaba, Hiroto, additional, Carroll, William, additional, Ramirez, Nilsa, additional, Philips, Aaron, additional, Kriwacki, Richard, additional, Yang, Jun, additional, Vincent, Tiffaney, additional, Loh, Mignon, additional, Rampersaud, Evadnie, additional, Raetz, Elizabeth, additional, Hunger, Stephen, additional, Tan, Kai, additional, Chang, Ti-Cheng, additional, Wu, Gang, additional, Pounds, Stanley, additional, and Teachey, David, additional

Published
2023
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16. Alu Elements and Hominid Phylogenetics

Author

Salem, Abdel-Halim, Ray, David A., Xing, Jinchuan, Callinan, Pauline A., Myers, Jeremy S., Hedges, Dale J., Garber, Randall K., Witherspoon, David J., Jorde, Lynn B., and Batzer, Mark A.

Published
2003

17. Clinical and Genomic Features of Patients with Renal Cell Carcinoma and Advanced Chronic Kidney Disease: Analysis of a Multi-Institutional Database.

Author

Eule, Corbin J., Hu, Junxiao, Hedges, Dale, Jani, Alkesh, Pshak, Thomas, Manley, Brandon J., Sanchez, Alejandro, Dreicer, Robert, Myint, Zin W., Zakharia, Yousef, and Lam, Elaine T.

Subjects
CHRONIC kidney failure complications, RISK assessment, CREATININE, RESEARCH funding, CANCER patients, SYMPTOMS, DESCRIPTIVE statistics, MULTIVARIATE analysis, GENES, ODDS ratio, RENAL cell carcinoma, GENETIC mutation, OVERALL survival, DISEASE risk factors
Abstract

Simple Summary: Despite the increased risk of developing renal cell carcinoma (RCC) in patients with advanced chronic kidney disease (ACKD), little is known about the patient clinical characteristics and genetic mutations found in these RCC tumors. Using a multi-institutional research network, this study compiled clinical records and somatic tumor whole exome sequencing data of 296 adult patients with RCC, 61 of whom had ACKD. Patients with RCC and ACKD were more likely to be male, present with earlier stage RCC at diagnosis, and have lower rates of BAP1 mutations. Median overall survival was not reached in either group over a median follow-up of 31.3 months. These findings suggest RCC in patients with ACKD develops via a BAP1-independent mutational driver and further support BAP1 loss as a marker of disease aggressiveness. Background: Patients with advanced chronic kidney disease (ACKD) are at an increased risk of developing renal cell carcinoma (RCC), but molecular alterations in RCC specimens arising from ACKD and overall survival (OS) in affected patients are not well defined. Patients and Methods: Using the Oncology Research Information Exchange Network (ORIEN) Total Cancer Care® protocol, 296 consented adult patients with RCC and somatic tumor whole exome sequencing were included. Patients with ACKD were defined as those with serum creatinine ≥1.5 mg/dL prior to RCC diagnosis. Results: Of 296 patients with RCC, 61 met the criteria for ACKD. The most common somatic mutations in the overall cohort were in VHL (126, 42.6%), PBRM1 (102, 34.5%), and SETD2 (54, 18.2%). BAP1 had a decreased mutational frequency in RCC specimens from patients without ACKD as compared to those with ACKD (10.6% versus 1.6%), but this was not statistically significant in univariable (OR 0.14, p = 0.056) or multivariable (OR 0.15, p = 0.067) analysis. Median OS was not reached in either cohort. Conclusions: Using the clinicogenomic ORIEN database, our study found lower rates of BAP1 mutations in RCC specimens from patients with ACKD, which may reflect a BAP1-independent mutational driver of RCC in patients with ACKD. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Data from Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing

Author

Newman, Scott, primary, Nakitandwe, Joy, primary, Kesserwan, Chimene A., primary, Azzato, Elizabeth M., primary, Wheeler, David A., primary, Rusch, Michael, primary, Shurtleff, Sheila, primary, Hedges, Dale J., primary, Hamilton, Kayla V., primary, Foy, Scott G., primary, Edmonson, Michael N., primary, Thrasher, Andrew, primary, Bahrami, Armita, primary, Orr, Brent A., primary, Klco, Jeffery M., primary, Gu, Jiali, primary, Harrison, Lynn W., primary, Wang, Lu, primary, Clay, Michael R., primary, Ouma, Annastasia, primary, Silkov, Antonina, primary, Liu, Yanling, primary, Zhang, Zhaojie, primary, Liu, Yu, primary, Brady, Samuel W., primary, Zhou, Xin, primary, Chang, Ti-Cheng, primary, Pande, Manjusha, primary, Davis, Eric, primary, Becksfort, Jared, primary, Patel, Aman, primary, Wilkinson, Mark R., primary, Rahbarinia, Delaram, primary, Kubal, Manish, primary, Maciaszek, Jamie L., primary, Pastor, Victor, primary, Knight, Jay, primary, Gout, Alexander M., primary, Wang, Jian, primary, Gu, Zhaohui, primary, Mullighan, Charles G., primary, McGee, Rose B., primary, Quinn, Emily A., primary, Nuccio, Regina, primary, Mostafavi, Roya, primary, Gerhardt, Elsie L., primary, Taylor, Leslie M., primary, Valdez, Jessica M., primary, Hines-Dowell, Stacy J., primary, Pappo, Alberto S., primary, Robinson, Giles, primary, Johnson, Liza-Marie, primary, Pui, Ching-Hon, primary, Ellison, David W., primary, Downing, James R., primary, Zhang, Jinghui, primary, and Nichols, Kim E., primary

Published
2023
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19. Supplementary Figure S2 from Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing

Author

Newman, Scott, primary, Nakitandwe, Joy, primary, Kesserwan, Chimene A., primary, Azzato, Elizabeth M., primary, Wheeler, David A., primary, Rusch, Michael, primary, Shurtleff, Sheila, primary, Hedges, Dale J., primary, Hamilton, Kayla V., primary, Foy, Scott G., primary, Edmonson, Michael N., primary, Thrasher, Andrew, primary, Bahrami, Armita, primary, Orr, Brent A., primary, Klco, Jeffery M., primary, Gu, Jiali, primary, Harrison, Lynn W., primary, Wang, Lu, primary, Clay, Michael R., primary, Ouma, Annastasia, primary, Silkov, Antonina, primary, Liu, Yanling, primary, Zhang, Zhaojie, primary, Liu, Yu, primary, Brady, Samuel W., primary, Zhou, Xin, primary, Chang, Ti-Cheng, primary, Pande, Manjusha, primary, Davis, Eric, primary, Becksfort, Jared, primary, Patel, Aman, primary, Wilkinson, Mark R., primary, Rahbarinia, Delaram, primary, Kubal, Manish, primary, Maciaszek, Jamie L., primary, Pastor, Victor, primary, Knight, Jay, primary, Gout, Alexander M., primary, Wang, Jian, primary, Gu, Zhaohui, primary, Mullighan, Charles G., primary, McGee, Rose B., primary, Quinn, Emily A., primary, Nuccio, Regina, primary, Mostafavi, Roya, primary, Gerhardt, Elsie L., primary, Taylor, Leslie M., primary, Valdez, Jessica M., primary, Hines-Dowell, Stacy J., primary, Pappo, Alberto S., primary, Robinson, Giles, primary, Johnson, Liza-Marie, primary, Pui, Ching-Hon, primary, Ellison, David W., primary, Downing, James R., primary, Zhang, Jinghui, primary, and Nichols, Kim E., primary

Published
2023
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20. Supplementary Tables from Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing

Author

Newman, Scott, primary, Nakitandwe, Joy, primary, Kesserwan, Chimene A., primary, Azzato, Elizabeth M., primary, Wheeler, David A., primary, Rusch, Michael, primary, Shurtleff, Sheila, primary, Hedges, Dale J., primary, Hamilton, Kayla V., primary, Foy, Scott G., primary, Edmonson, Michael N., primary, Thrasher, Andrew, primary, Bahrami, Armita, primary, Orr, Brent A., primary, Klco, Jeffery M., primary, Gu, Jiali, primary, Harrison, Lynn W., primary, Wang, Lu, primary, Clay, Michael R., primary, Ouma, Annastasia, primary, Silkov, Antonina, primary, Liu, Yanling, primary, Zhang, Zhaojie, primary, Liu, Yu, primary, Brady, Samuel W., primary, Zhou, Xin, primary, Chang, Ti-Cheng, primary, Pande, Manjusha, primary, Davis, Eric, primary, Becksfort, Jared, primary, Patel, Aman, primary, Wilkinson, Mark R., primary, Rahbarinia, Delaram, primary, Kubal, Manish, primary, Maciaszek, Jamie L., primary, Pastor, Victor, primary, Knight, Jay, primary, Gout, Alexander M., primary, Wang, Jian, primary, Gu, Zhaohui, primary, Mullighan, Charles G., primary, McGee, Rose B., primary, Quinn, Emily A., primary, Nuccio, Regina, primary, Mostafavi, Roya, primary, Gerhardt, Elsie L., primary, Taylor, Leslie M., primary, Valdez, Jessica M., primary, Hines-Dowell, Stacy J., primary, Pappo, Alberto S., primary, Robinson, Giles, primary, Johnson, Liza-Marie, primary, Pui, Ching-Hon, primary, Ellison, David W., primary, Downing, James R., primary, Zhang, Jinghui, primary, and Nichols, Kim E., primary

Published
2023
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21. Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome

Author

Rusch, Michael, Nakitandwe, Joy, Shurtleff, Sheila, Newman, Scott, Zhang, Zhaojie, Edmonson, Michael N., Parker, Matthew, Jiao, Yuannian, Ma, Xiaotu, Liu, Yanling, Gu, Jiali, Walsh, Michael F., Becksfort, Jared, Thrasher, Andrew, Li, Yongjin, McMurry, James, Hedlund, Erin, Patel, Aman, Easton, John, Yergeau, Donald, Vadodaria, Bhavin, Tatevossian, Ruth G., Raimondi, Susana, Hedges, Dale, Chen, Xiang, Hagiwara, Kohei, McGee, Rose, Robinson, Giles W., Klco, Jeffery M., Gruber, Tanja A., Ellison, David W., Downing, James R, and Zhang, Jinghui

Published
2018
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22. Comprehensive Genome Characterization of Childhood T-ALL Links Oncogene Activation Mechanism and Subtypes to Prognosis

Author

Pölönen, Petri, primary, Elsayed, Abdelrahman, additional, Di Giacomo, Danika, additional, Montefiori, Lindsey, additional, Kimura, Shunsuke, additional, Myers, Jason, additional, Hedges, Dale, additional, Xu, Jason, additional, Hui, Yawei, additional, Cheng, Zhongshan, additional, Fan, Yiping, additional, Iacobucci, Ilaria, additional, Chang, Yunchao, additional, Shraim, Rawan, additional, Devidas, Meenakshi, additional, Winter, Stuart S., additional, Dunsmore, Kimberly P., additional, Yang, Jun J.J., additional, Vincent, Tiffaney L., additional, Tan, Kai, additional, Chen, Changya, additional, Newman, Haley, additional, Loh, Mignon L., additional, Raetz, Elizabeth A., additional, Hunger, Stephen P., additional, Rampersaud, Evadnie, additional, Chang, Ti-Cheng, additional, Wu, Gang, additional, Pounds, Stanley B., additional, Mullighan, Charles G., additional, and Teachey, David T., additional

Published
2022
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23. 1147 Differences in co-expression of T cell co-inhibitory and co-stimulatory molecules with PD1 across different human cancers

Author

Tarhini, Ahmad, primary, Hedges, Dale, additional, Tan, Aik Choon, additional, Rodriguez, Paulo, additional, Sukrithan, Vineeth, additional, Ratan, Aakrosh, additional, McCarter, Martin, additional, Carpten, John, additional, Colman, Howard, additional, Ikeguchi, Alexandra, additional, Puzanov, Igor, additional, Arnold, Susanne, additional, Churchman, Michelle, additional, Hwu, Patrick, additional, Conejo-Garcia, Jose, additional, Dalton, William (Bill), additional, and Weiner, George, additional

Published
2022
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24. Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia

Author

Ryan, Sarra, primary, Peden, John, additional, Kingsbury, Zoya, additional, Schwab, Claire, additional, James, Terena, additional, Polonen, Petri, additional, Mijuskovic, Martina, additional, Becq, Jennifer, additional, Yim, Richard, additional, Cranston, Ruth, additional, Hedges, Dale, additional, Roberts, Kathryn, additional, Mullighan, Charles, additional, Vora, Ajay, additional, Russell, Lisa, additional, Moorman, Anthony, additional, Bentley, David, additional, Harrison, Christine, additional, and Ross, Mark, additional

Published
2022
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25. Genome-wide analysis of the human Alu Yb-lineage

Author

Carter Anthony B, Salem Abdel-Halim, Hedges Dale J, Keegan Catherine, Kimball Beth, Walker Jerilyn A, Watkins W, Jorde Lynn B, and Batzer Mark A

Subjects
mobile elements, SINEs, Medicine, Genetics, QH426-470
Abstract

Abstract The Alu Yb-lineage is a 'young' primarily human-specific group of short interspersed element (SINE) subfamilies that have integrated throughout the human genome. In this study, we have computationally screened the draft sequence of the human genome for Alu Yb-lineage subfamily members present on autosomal chromosomes. A total of 1,733 Yb Alu subfamily members have integrated into human autosomes. The average ages of Yb-lineage subfamilies, Yb7, Yb8 and Yb9, are estimated as 4.81, 2.39 and 2.32 million years, respectively. In order to determine the contribution of the Alu Yb-lineage to human genomic diversity, 1,202 loci were analysed using polymerase chain reaction (PCR)-based assays, which amplify the genomic regions containing individual Yb-lineage subfamily members. Approximately 20 per cent of the Yb-lineage Alu elements are polymorphic for insertion presence/absence in the human genome. Fewer than 0.5 per cent of the Yb loci also demonstrate insertions at orthologous positions in non-human primate genomes. Genomic sequencing of these unusual loci demonstrates that each of the orthologous loci from non-human primate genomes contains older Y, Sg and Sx Alu family members that have been altered, through various mechanisms, into Yb8 sequences. These data suggest that Alu Yb-lineage subfamily members are largely restricted to the human genome. The high copy number, level of insertion polymorphism and estimated age indicate that members of the Alu Yb elements will be useful in a wide range of genetic analyses.

Published
2004
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26. Germline Mutations in Predisposition Genes in Pediatric Cancer

Author

Zhang, Jinghui, Walsh, Michael F., Wu, Gang, Edmonson, Michael N., Gruber, Tanja A., Easton, John, Hedges, Dale, Ma, Xiaotu, Zhou, Xin, Yergeau, Donald A., Wilkinson, Mark R., Vadodaria, Bhavin, Chen, Xiang, McGee, Rose B., Hines-Dowell, Stacy, Nuccio, Regina, Quinn, Emily, Shurtleff, Sheila A., Rusch, Michael, Patel, Aman, Becksfort, Jared B., Wang, Shuoguo, Weaver, Meaghann S., Ding, Li, Mardis, Elaine R., Wilson, Richard K., Gajjar, Amar, Ellison, David W., Pappo, Alberto S., Pui, Ching-Hon, Nichols, Kim E., and Downing, James R.

Published
2015
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27. Author Reply to Peer Reviews of CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes

Author

Xu, Beisi, primary, Wu, Gang, additional, Fan, Yiping, additional, Schreiner, Patrick, additional, Hedges, Dale, additional, Jin, Hongjian, additional, Hui, Yawei, additional, Kanneganti, Thirumala-Devi, additional, Peng, Jamy C., additional, Rosikiewicz, Wojciech, additional, and Djekidel, Mohamed Nadhir, additional

Published
2021
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29. Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing

Author

Newman, Scott, primary, Nakitandwe, Joy, additional, Kesserwan, Chimene A., additional, Azzato, Elizabeth M., additional, Wheeler, David A., additional, Rusch, Michael, additional, Shurtleff, Sheila, additional, Hedges, Dale J., additional, Hamilton, Kayla V., additional, Foy, Scott G., additional, Edmonson, Michael N., additional, Thrasher, Andrew, additional, Bahrami, Armita, additional, Orr, Brent A., additional, Klco, Jeffery M., additional, Gu, Jiali, additional, Harrison, Lynn W., additional, Wang, Lu, additional, Clay, Michael R., additional, Ouma, Annastasia, additional, Silkov, Antonina, additional, Liu, Yanling, additional, Zhang, Zhaojie, additional, Liu, Yu, additional, Brady, Samuel W., additional, Zhou, Xin, additional, Chang, Ti-Cheng, additional, Pande, Manjusha, additional, Davis, Eric, additional, Becksfort, Jared, additional, Patel, Aman, additional, Wilkinson, Mark R., additional, Rahbarinia, Delaram, additional, Kubal, Manish, additional, Maciaszek, Jamie L., additional, Pastor, Victor, additional, Knight, Jay, additional, Gout, Alexander M., additional, Wang, Jian, additional, Gu, Zhaohui, additional, Mullighan, Charles G., additional, McGee, Rose B., additional, Quinn, Emily A., additional, Nuccio, Regina, additional, Mostafavi, Roya, additional, Gerhardt, Elsie L., additional, Taylor, Leslie M., additional, Valdez, Jessica M., additional, Hines-Dowell, Stacy J., additional, Pappo, Alberto S., additional, Robinson, Giles, additional, Johnson, Liza-Marie, additional, Pui, Ching-Hon, additional, Ellison, David W., additional, Downing, James R., additional, Zhang, Jinghui, additional, and Nichols, Kim E., additional

Published
2021
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30. Abstract 642: Genomes for Kids: Comprehensive DNA and RNA sequencing defining the scope of actionable mutations in pediatric cancer

Author

Wheeler, David A., primary, Newman, Scott, additional, Nakitandwe, Joy, additional, Kesserwan, Chimene A., additional, Azzato, Elizabeth M., additional, Rusch, Michael C., additional, Shurtleff, Sheila, additional, Bahrami, Armita, additional, Orr, Brent, additional, Klco, Jeffery M., additional, Hedges, Dale J., additional, Hamilton, Kayla V., additional, Foy, Scott G., additional, Edmonson, Michael N., additional, Thrasher, Andrew, additional, Gu, Jiali, additional, Harrison, Lynn W., additional, Wang, Lu, additional, Mostafavi, Roya, additional, Kubal, Manish, additional, Maciaszek, Jamie, additional, Clay, Michael, additional, Ouma, Annastasia, additional, Silkov, Antonina, additional, Liu, Yanling, additional, Zhang, Zhaojie, additional, Liu, Yu, additional, Brady, Samuel W., additional, Zhou, Xin, additional, Wilkinson, Mark, additional, Rahbarinia, Delaram, additional, Knight, Jay, additional, Wang, Jian, additional, Mullighan, Charles G., additional, McGee, Rose B., additional, Quinn, Emily A., additional, Gerhardt, Elsie L., additional, Taylor, Leslie M., additional, Nuccio, Regina, additional, Valdez, Jessica M., additional, Hines-Dowell, Stacy J., additional, Pappo, Alberto, additional, Robinson, Giles, additional, Johnson, Liza-Marie, additional, Pui, Ching-Hon, additional, Ellison, David W., additional, Downing, James R., additional, Zhang, Jinghui, additional, and Nichols, Kim E., additional

Published
2021
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32. From the margins of the genome: Mobile elements shape primate evolution

Author

Hedges, Dale J. and Batzer, Mark A.

Subjects
Primates -- Genetic aspects, Molecular genetics -- Research, Genomes -- Research, Biological sciences
Abstract

The advances in the understanding of the host-mobile element dynamic and its overall impact on primate evolution are reviewed. Primate genomes are inundated with repetitive sequence that consists of 'molecular fossils' inherited from early mammalian ancestors and a significant portion of this material comprises active mobile element lineages.

Published
2005

36. Evaluating Mitochondrial DNA Variation in Autism Spectrum Disorders

Author

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

Published
2013
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37. Age at onset in two common neurodegenerative diseases is genetically controlled

Author

Li, Yi-Ju, Scott, William K., Hedges, Dale J., Zhang, Fengyu, Gaskell, P. Craig, Nance, Martha A., Watts, Ray L., Hubble, Jean P., Koller, William C., Pahwa, Rajesh, Stern, Matthew B., Hiner, Bradley C., Jankovic, Joseph, Allen, Fred H., Jr., Goetz, Christopher G., Mastaglia, Frank, Stajich, Jeffrey M., Gibson, Rachel A., Middleton, Lefkos T., Saunders, Ann M., Scott, Burton L., Small, Gary W., Nicodemus, Kristin K., Reed, Allison D., Schmechel, Donald E., Welsh-Bohmer, Kathleen A., Conneally, P. Michael, Roses, Allen D., Gilbert, John R., Vance, Jeffery M., Haines, Jonathan L., and Pericak-Vance, Margaret A.

Subjects
Human genetics -- Research, Nervous system -- Degeneration, Alzheimer's disease -- Genetic aspects, Parkinson's disease -- Genetic aspects, Biological sciences
Published
2002

38. HGG-57. WHOLE-GENOME SEQUENCING, METHYLATION ANALYSIS, AND SINGLE-CELL RNA-SEQ DEFINE UNIQUE CHARACTERISTICS OF PEDIATRIC TREATMENT-INDUCED HIGH-GRADE GLIOMA AND SUGGEST ONCOGENIC MECHANISMS

Author

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

Published
2020
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40. A Genome-wide Association Study of Autism Reveals a Common Novel Risk Locus at 5p14.1

Author

Ma, Deqiong, Salyakina, Daria, Jaworski, James M., Konidari, Ioanna, Whitehead, Patrice L., Andersen, Ashley N., Hoffman, Joshua D., Slifer, Susan H., Hedges, Dale J., Cukier, Holly N., Griswold, Anthony J., McCauley, Jacob L., Beecham, Gary W., Wright, Harry H., Abramson, Ruth K., Martin, Eden R., Hussman, John P., Gilbert, John R., Cuccaro, Michael L., Haines, Jonathan L., and Pericak-Vance, Margaret A.

Published
2009
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42. Alu insertion loci and platyrrhine primate phylogeny

Author

Ray, David A., Xing, Jinchuan, Hedges, Dale J., Hall, Michael A., Laborde, Meredith E., Anders, Bridget A., White, Brittany R., Stoilova, Nadica, Fowlkes, Justin D., Landry, Kate E., Chemnick, Leona G., Ryder, Oliver A., and Batzer, Mark A.

Published
2005
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49. Analysis of the Human Alu Ya-lineage

Author

Otieno, Anthony C., Carter, Anthony B., Hedges, Dale J., Walker, Jerilyn A., Ray, David A., Garber, Randall K., Anders, Bridget A., Stoilova, Nadica, Laborde, Meredith E., Fowlkes, Justin D., Huang, Cheney H., Perodeau, Benjamin, and Batzer, Mark A.

Published
2004
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50. Estimated number of adult survivors of childhood cancer in United States with cancer‐predisposing germline variants

Author

Wilson, Carmen L., primary, Wang, Zhaoming, additional, Liu, Qi, additional, Ehrhardt, Matthew J., additional, Mostafavi, Roya, additional, Easton, John, additional, Mulder, Heather, additional, Hedges, Dale J., additional, Wang, Shuoguo, additional, Rusch, Michael, additional, Edmonson, Michael, additional, Levy, Shawn, additional, Lanctot, Jennifer Q., additional, Currie, Kelsey, additional, Lear, Matthew, additional, Patel, Aman, additional, Sapkota, Yadav, additional, Brooke, Russell J., additional, Moon, Wonjong, additional, Chang, Ti‐Cheng, additional, Chen, Wenan, additional, Kesserwan, Chimene A., additional, Wu, Gang, additional, Nichols, Kim E., additional, Hudson, Melissa M., additional, Zhang, Jinghui, additional, Robison, Leslie L., additional, and Yasui, Yutaka, additional

Published
2019
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