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39 results on '"Gout, A. M."'

1. Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication

Author

Liu, Yanling, Klein, Jonathon, Bajpai, Richa, Dong, Li, Tran, Quang, Kolekar, Pandurang, Smith, Jenny L, Ries, Rhonda E, Huang, Benjamin J, Wang, Yi-Cheng, Alonzo, Todd A, Tian, Liqing, Mulder, Heather L, Shaw, Timothy I, Ma, Jing, Walsh, Michael P, Song, Guangchun, Westover, Tamara, Autry, Robert J, Gout, Alexander M, Wheeler, David A, Wan, Shibiao, Wu, Gang, Yang, Jun J, Evans, William E, Loh, Mignon, Easton, John, Zhang, Jinghui, Klco, Jeffery M, Meshinchi, Soheil, Brown, Patrick A, Pruett-Miller, Shondra M, and Ma, Xiaotu

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Human Genome, Biotechnology, Pediatric Research Initiative, Pediatric Cancer, Rare Diseases, Cancer, Pediatric, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Aetiology, 2.1 Biological and endogenous factors, Humans, Child, Core Binding Factor Alpha 2 Subunit, Oncogene Fusion, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Transcriptome, Causality, Oncogene Proteins, Fusion
Abstract

Oncogenic fusions formed through chromosomal rearrangements are hallmarks of childhood cancer that define cancer subtype, predict outcome, persist through treatment, and can be ideal therapeutic targets. However, mechanistic understanding of the etiology of oncogenic fusions remains elusive. Here we report a comprehensive detection of 272 oncogenic fusion gene pairs by using tumor transcriptome sequencing data from 5190 childhood cancer patients. We identify diverse factors, including translation frame, protein domain, splicing, and gene length, that shape the formation of oncogenic fusions. Our mathematical modeling reveals a strong link between differential selection pressure and clinical outcome in CBFB-MYH11. We discover 4 oncogenic fusions, including RUNX1-RUNX1T1, TCF3-PBX1, CBFA2T3-GLIS2, and KMT2A-AFDN, with promoter-hijacking-like features that may offer alternative strategies for therapeutic targeting. We uncover extensive alternative splicing in oncogenic fusions including KMT2A-MLLT3, KMT2A-MLLT10, C11orf95-RELA, NUP98-NSD1, KMT2A-AFDN and ETV6-RUNX1. We discover neo splice sites in 18 oncogenic fusion gene pairs and demonstrate that such splice sites confer therapeutic vulnerability for etiology-based genome editing. Our study reveals general principles on the etiology of oncogenic fusions in childhood cancer and suggests profound clinical implications including etiology-based risk stratification and genome-editing-based therapeutics.

Published
2023

2. “I Knew It Was Wrong the Moment I Got the Order”: A Narrative Thematic Analysis of Moral Injury in Combat Veterans

Author

Held, Philip, Klassen, Brian J, Hall, Joanne M, Friese, Tanya R, Bertsch-Gout, Marcel M, Zalta, Alyson K, and Pollack, Mark H

Subjects
Adaptation, Psychological, Adult, Alcoholism, Decision Making, Hierarchy, Social, Humans, Interviews as Topic, Male, Middle Aged, Morals, Narration, Stress, Psychological, Veterans, War Exposure, moral injury, trauma, veterans, military, narrative thematic analysis, Psychology
Abstract

ObjectiveMoral injury is a nascent construct intended to capture reactions to events that violate deeply held beliefs and moral values. Although a model of moral injury has been proposed, many of the theoretical propositions of this model have yet to be systematically studied.MethodWe conducted semistructured interviews with eight veterans who reported experiencing morally injurious events during war zone deployments.ResultsUsing narrative thematic analysis, five main themes and associated subthemes emerged from the data. The main themes capture the timing of the event, contextual factors that affected the decision-making process during the morally injurious event, reactions to the moral injurious event, search for purpose and meaning, and opening up.ConclusionThe findings from the present study supported an existing model of moral injury, while extending it in several important ways. Preliminary clinical recommendations and directions for future research are discussed based on the study findings. These include directly exploring the context surrounding the morally injurious event, examining the veterans' moral appraisals, and helping them assume appropriate responsibility for their actions to reduce excessive self-blame. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Published
2019

7. Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations

Author

Brady, Samuel W., Liu, Yanling, Ma, Xiaotu, Gout, Alexander M., Hagiwara, Kohei, Zhou, Xin, Wang, Jian, Macias, Michael, Chen, Xiaolong, Easton, John, Mulder, Heather L., Rusch, Michael, Wang, Lu, Nakitandwe, Joy, Lei, Shaohua, Davis, Eric M., Naranjo, Arlene, Cheng, Cheng, Maris, John M., Downing, James R., Cheung, Nai-Kong V., Hogarty, Michael D., Dyer, Michael A., and Zhang, Jinghui

Published
2020
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8. 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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9. 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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10. Data from St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem

Author

McLeod, Clay, primary, Gout, Alexander M., primary, Zhou, Xin, primary, Thrasher, Andrew, primary, Rahbarinia, Delaram, primary, Brady, Samuel W., primary, Macias, Michael, primary, Birch, Kirby, primary, Finkelstein, David, primary, Sunny, Jobin, primary, Mudunuri, Rahul, primary, Orr, Brent A., primary, Treadway, Madison, primary, Davidson, Bob, primary, Ard, Tracy K., primary, Chiao, Arthur, primary, Swistak, Andrew, primary, Wiggins, Stephanie, primary, Foy, Scott, primary, Wang, Jian, primary, Sioson, Edgar, primary, Wang, Shuoguo, primary, Michael, J. Robert, primary, Liu, Yu, primary, Ma, Xiaotu, primary, Patel, Aman, primary, Edmonson, Michael N., primary, Wilkinson, Mark R., primary, Frantz, Andrew M., primary, Chang, Ti-Cheng, primary, Tian, Liqing, primary, Lei, Shaohua, primary, Islam, S.M. Ashiqul, primary, Meyer, Christopher, primary, Thangaraj, Naina, primary, Tater, Pamella, primary, Kandali, Vijay, primary, Ma, Singer, primary, Nguyen, Tuan, primary, Serang, Omar, primary, McGuire, Irina, primary, Robison, Nedra, primary, Gentry, Darrell, primary, Tang, Xing, primary, Palmer, Lance E., primary, Wu, Gang, primary, Suh, Ed, primary, Tanner, Leigh, primary, McMurry, James, primary, Lear, Matthew, primary, Pappo, Alberto S., primary, Wang, Zhaoming, primary, Wilson, Carmen L., primary, Cheng, Yong, primary, Meshinchi, Soheil, primary, Alexandrov, Ludmil B., primary, Weiss, Mitchell J., primary, Armstrong, Gregory T., primary, Robison, Leslie L., primary, Yasui, Yutaka, primary, Nichols, Kim E., primary, Ellison, David W., primary, Bangur, Chaitanya, primary, Mullighan, Charles G., primary, Baker, Suzanne J., primary, Dyer, Michael A., primary, Miller, Geralyn, primary, Newman, Scott, primary, Rusch, Michael, primary, Daly, Richard, primary, Perry, Keith, primary, Downing, James R., primary, and Zhang, Jinghui, primary

Published
2023
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11. 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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12. Supplementary Tables from St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem

Author

McLeod, Clay, primary, Gout, Alexander M., primary, Zhou, Xin, primary, Thrasher, Andrew, primary, Rahbarinia, Delaram, primary, Brady, Samuel W., primary, Macias, Michael, primary, Birch, Kirby, primary, Finkelstein, David, primary, Sunny, Jobin, primary, Mudunuri, Rahul, primary, Orr, Brent A., primary, Treadway, Madison, primary, Davidson, Bob, primary, Ard, Tracy K., primary, Chiao, Arthur, primary, Swistak, Andrew, primary, Wiggins, Stephanie, primary, Foy, Scott, primary, Wang, Jian, primary, Sioson, Edgar, primary, Wang, Shuoguo, primary, Michael, J. Robert, primary, Liu, Yu, primary, Ma, Xiaotu, primary, Patel, Aman, primary, Edmonson, Michael N., primary, Wilkinson, Mark R., primary, Frantz, Andrew M., primary, Chang, Ti-Cheng, primary, Tian, Liqing, primary, Lei, Shaohua, primary, Islam, S.M. Ashiqul, primary, Meyer, Christopher, primary, Thangaraj, Naina, primary, Tater, Pamella, primary, Kandali, Vijay, primary, Ma, Singer, primary, Nguyen, Tuan, primary, Serang, Omar, primary, McGuire, Irina, primary, Robison, Nedra, primary, Gentry, Darrell, primary, Tang, Xing, primary, Palmer, Lance E., primary, Wu, Gang, primary, Suh, Ed, primary, Tanner, Leigh, primary, McMurry, James, primary, Lear, Matthew, primary, Pappo, Alberto S., primary, Wang, Zhaoming, primary, Wilson, Carmen L., primary, Cheng, Yong, primary, Meshinchi, Soheil, primary, Alexandrov, Ludmil B., primary, Weiss, Mitchell J., primary, Armstrong, Gregory T., primary, Robison, Leslie L., primary, Yasui, Yutaka, primary, Nichols, Kim E., primary, Ellison, David W., primary, Bangur, Chaitanya, primary, Mullighan, Charles G., primary, Baker, Suzanne J., primary, Dyer, Michael A., primary, Miller, Geralyn, primary, Newman, Scott, primary, Rusch, Michael, primary, Daly, Richard, primary, Perry, Keith, primary, Downing, James R., primary, and Zhang, Jinghui, primary

Published
2023
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13. Supplementary Figures 1-7 from Malignant Progression of an Ancestral Bone Marrow Clone Harboring a CIC-NUTM2A Fusion in Isolated Myeloid Sarcoma

Author

Kamens, Jennifer L., primary, Dang, Jinjun, primary, Shaw, Timothy I., primary, Gout, Alexander M., primary, Newman, Scott, primary, Hagiwara, Kohei, primary, Smith, Amelia M.R., primary, Obermayer, Alyssa N., primary, Aldridge, Sarah, primary, Ma, Jing, primary, Zhang, Yang, primary, Wu, Gang, primary, Leventaki, Vasiliki, primary, Santiago, Teresa, primary, Raimondi, Susana, primary, Nakitandwe, Joy, primary, Pappo, Alberto, primary, Li, Chunliang, primary, Zhang, Jinghui, primary, and Gruber, Tanja A., primary

Published
2023
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14. Supplementary Data from St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem

Author

McLeod, Clay, primary, Gout, Alexander M., primary, Zhou, Xin, primary, Thrasher, Andrew, primary, Rahbarinia, Delaram, primary, Brady, Samuel W., primary, Macias, Michael, primary, Birch, Kirby, primary, Finkelstein, David, primary, Sunny, Jobin, primary, Mudunuri, Rahul, primary, Orr, Brent A., primary, Treadway, Madison, primary, Davidson, Bob, primary, Ard, Tracy K., primary, Chiao, Arthur, primary, Swistak, Andrew, primary, Wiggins, Stephanie, primary, Foy, Scott, primary, Wang, Jian, primary, Sioson, Edgar, primary, Wang, Shuoguo, primary, Michael, J. Robert, primary, Liu, Yu, primary, Ma, Xiaotu, primary, Patel, Aman, primary, Edmonson, Michael N., primary, Wilkinson, Mark R., primary, Frantz, Andrew M., primary, Chang, Ti-Cheng, primary, Tian, Liqing, primary, Lei, Shaohua, primary, Islam, S.M. Ashiqul, primary, Meyer, Christopher, primary, Thangaraj, Naina, primary, Tater, Pamella, primary, Kandali, Vijay, primary, Ma, Singer, primary, Nguyen, Tuan, primary, Serang, Omar, primary, McGuire, Irina, primary, Robison, Nedra, primary, Gentry, Darrell, primary, Tang, Xing, primary, Palmer, Lance E., primary, Wu, Gang, primary, Suh, Ed, primary, Tanner, Leigh, primary, McMurry, James, primary, Lear, Matthew, primary, Pappo, Alberto S., primary, Wang, Zhaoming, primary, Wilson, Carmen L., primary, Cheng, Yong, primary, Meshinchi, Soheil, primary, Alexandrov, Ludmil B., primary, Weiss, Mitchell J., primary, Armstrong, Gregory T., primary, Robison, Leslie L., primary, Yasui, Yutaka, primary, Nichols, Kim E., primary, Ellison, David W., primary, Bangur, Chaitanya, primary, Mullighan, Charles G., primary, Baker, Suzanne J., primary, Dyer, Michael A., primary, Miller, Geralyn, primary, Newman, Scott, primary, Rusch, Michael, primary, Daly, Richard, primary, Perry, Keith, primary, Downing, James R., primary, and Zhang, Jinghui, primary

Published
2023
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15. Supplementary Tables 1-5 from Malignant Progression of an Ancestral Bone Marrow Clone Harboring a CIC-NUTM2A Fusion in Isolated Myeloid Sarcoma

Author

Kamens, Jennifer L., primary, Dang, Jinjun, primary, Shaw, Timothy I., primary, Gout, Alexander M., primary, Newman, Scott, primary, Hagiwara, Kohei, primary, Smith, Amelia M.R., primary, Obermayer, Alyssa N., primary, Aldridge, Sarah, primary, Ma, Jing, primary, Zhang, Yang, primary, Wu, Gang, primary, Leventaki, Vasiliki, primary, Santiago, Teresa, primary, Raimondi, Susana, primary, Nakitandwe, Joy, primary, Pappo, Alberto, primary, Li, Chunliang, primary, Zhang, Jinghui, primary, and Gruber, Tanja A., primary

Published
2023
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16. Malignant Progression of an Ancestral Bone Marrow Clone Harboring a CIC-NUTM2A Fusion in Isolated Myeloid Sarcoma

Author

Kamens, Jennifer L., primary, Dang, Jinjun, additional, Shaw, Timothy I., additional, Gout, Alexander M., additional, Newman, Scott, additional, Hagiwara, Kohei, additional, Smith, Amelia M.R., additional, Obermayer, Alyssa N., additional, Aldridge, Sarah, additional, Ma, Jing, additional, Zhang, Yang, additional, Wu, Gang, additional, Leventaki, Vasiliki, additional, Santiago, Teresa, additional, Raimondi, Susana, additional, Nakitandwe, Joy, additional, Pappo, Alberto, additional, Li, Chunliang, additional, Zhang, Jinghui, additional, and Gruber, Tanja A., additional

Published
2023
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17. Abstract 1901: VisComm: A cloud-based platform for accessing and creating scientific visualization for the pediatric cancer research community

Author

Finkelstein, David B., primary, Madson, James, additional, Vacaroiu, Lucian, additional, Gout, Alexander M., additional, Hirja, Leonard, additional, Sandor, Stephanie, additional, Thrasher, Andrew, additional, Reilly, Colleen, additional, Wang, Jian, additional, Chen, Xiaolong, additional, Zhou, Xin, additional, Zhang, Jinghui, additional, and McLeod, Clay, additional

Published
2022
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20. Polygenic Risk Score Improves Risk Stratification and Prediction of Subsequent Thyroid Cancer after Childhood Cancer

Author

Song, Nan, primary, Liu, Qi, additional, Wilson, Carmen L., additional, Sapkota, Yadav, additional, Ehrhardt, Matthew J., additional, Gibson, Todd M., additional, Morton, Lindsay M., additional, Chanock, Stephen J., additional, Neglia, Joseph P., additional, Arnold, Michael A., additional, Michael, J. Robert, additional, Gout, Alexander M., additional, Mulder, Heather L., additional, Easton, John, additional, Bhatia, Smita, additional, Armstrong, Gregory T., additional, Zhang, Jinghui, additional, Delaney, Angela, additional, Hudson, Melissa M., additional, Robison, Leslie L., additional, Yasui, Yutaka, additional, and Wang, Zhaoming, additional

Published
2021
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21. Additional file 1 of SequencErr: measuring and suppressing sequencer errors in next-generation sequencing data

Author

Davis, Eric M., Sun, Yu, Yanling Liu, Pandurang Kolekar, Shao, Ying, Szlachta, Karol, Mulder, Heather L., Dongren Ren, Rice, Stephen V., Zhaoming Wang, Nakitandwe, Joy, Gout, Alexander M., Shaner, Bridget, Hall, Salina, Robison, Leslie L., Pounds, Stanley, Klco, Jeffery M., Easton, John, and Ma, Xiaotu

Abstract

Additional file 1: Supplementary Figure S1. Minimal sample effect for calculating error rates for flow cells. Supplementary Figure S2. Flow cell-level error rate of all sequencers analyzed in this study. Supplementary Figure S3. Physical location pattern of tile-level error rates across flow cells in an outlier sequencer. Supplementary Figure S4. Prevalence of outlier tiles at flow cell level. Supplementary Figure S5. Positional pattern of problematic tiles. Supplementary Figure S6. Comparison of sequencers by using a common reference DNA library. Supplementary Figure S7. Effect of removing outlier tiles on the overall sequencing error rate. Supplementary Figure S8. Effect of removing outlier tiles evaluated by fold change. Supplementary Figure S9. Benchmarking SequencErr with FastQC. Supplementary Figure S10. Effect of DNA sequencing features on sequencer error rate. Supplementary Figure S11. Comparison of SequencErr with error correction methods. Supplementary Figure S12. Application of SequencErr on non-human dataset (SARS-CoV-2). Supplementary Note 1. Illustration of flowcell architecture. Supplementary Note 2. Manually checking read name information from NCBI SRA. Supplementary Note 3. Manually checking NCBI SRA database for the suitability of public datasets for our analysis. Supplementary Note 4. Flow cell layout of HiSeq. Supplementary Note 5. Flow cell layout of NextSeq. Supplementary Note 6. Flow cell layout of NovaSeq.

Published
2021
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22. 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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23. Abstract 2289: Empowering point-and-click genomic analysis with large pediatric genomic reference data on St. Jude Cloud

Author

Thrasher, Andrew, primary, Macias, Michael, additional, Gout, Alexander M., additional, Rahbarinia, Delaram, additional, Zhou, Xin, additional, Brady, Samuel W., additional, McLeod, Clay, additional, Rusch, Michael C., additional, Chen, Xiaolong, additional, Meshinchi, Soheil, additional, Dyer, Michael A., additional, Baker, Suzanne J., additional, Roussel, Martine F., additional, and Zhang, Jinghui, additional

Published
2021
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24. St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem

Author

McLeod, Clay, primary, Gout, Alexander M., additional, Zhou, Xin, additional, Thrasher, Andrew, additional, Rahbarinia, Delaram, additional, Brady, Samuel W., additional, Macias, Michael, additional, Birch, Kirby, additional, Finkelstein, David, additional, Sunny, Jobin, additional, Mudunuri, Rahul, additional, Orr, Brent A., additional, Treadway, Madison, additional, Davidson, Bob, additional, Ard, Tracy K., additional, Chiao, Arthur, additional, Swistak, Andrew, additional, Wiggins, Stephanie, additional, Foy, Scott, additional, Wang, Jian, additional, Sioson, Edgar, additional, Wang, Shuoguo, additional, Michael, J. Robert, additional, Liu, Yu, additional, Ma, Xiaotu, additional, Patel, Aman, additional, Edmonson, Michael N., additional, Wilkinson, Mark R., additional, Frantz, Andrew M., additional, Chang, Ti-Cheng, additional, Tian, Liqing, additional, Lei, Shaohua, additional, Islam, S.M. Ashiqul, additional, Meyer, Christopher, additional, Thangaraj, Naina, additional, Tater, Pamella, additional, Kandali, Vijay, additional, Ma, Singer, additional, Nguyen, Tuan, additional, Serang, Omar, additional, McGuire, Irina, additional, Robison, Nedra, additional, Gentry, Darrell, additional, Tang, Xing, additional, Palmer, Lance E., additional, Wu, Gang, additional, Suh, Ed, additional, Tanner, Leigh, additional, McMurry, James, additional, Lear, Matthew, additional, Pappo, Alberto S., additional, Wang, Zhaoming, additional, Wilson, Carmen L., additional, Cheng, Yong, additional, Meshinchi, Soheil, additional, Alexandrov, Ludmil B., additional, Weiss, Mitchell J., additional, Armstrong, Gregory T., additional, Robison, Leslie L., additional, Yasui, Yutaka, additional, Nichols, Kim E., additional, Ellison, David W., additional, Bangur, Chaitanya, additional, Mullighan, Charles G., additional, Baker, Suzanne J., additional, Dyer, Michael A., additional, Miller, Geralyn, additional, Newman, Scott, additional, Rusch, Michael, additional, Daly, Richard, additional, Perry, Keith, additional, Downing, James R., additional, and Zhang, Jinghui, additional

Published
2021
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25. St. Jude Cloud—a Pediatric Cancer Genomic Data Sharing Ecosystem

Author

McLeod, Clay, primary, Gout, Alexander M., additional, Zhou, Xin, additional, Rahbarinia, Delaram, additional, Thrasher, Andrew, additional, Newman, Scott, additional, Birch, Kirby, additional, Macias, Michael, additional, Finkelstein, David, additional, Sunny, Jobin, additional, Mudunuri, Rahul, additional, Orr, Brent A., additional, Treadway, Madison, additional, Davidson, Bob, additional, Ard, Tracy, additional, Swistak, Andrew, additional, Wiggins, Stephanie, additional, Foy, Scott, additional, Brady, Samuel W., additional, Wang, Jian, additional, Sioson, Edgar, additional, Wang, Shuoguo, additional, Michael, J. Robert, additional, Liu, Yu, additional, Ma, Xiaotu, additional, Patel, Aman, additional, Edmonson, Michael N., additional, Wilkinson, Mark R., additional, Frantz, Andrew, additional, Chang, Ti-Cheng, additional, Tian, Liqing, additional, Lei, Shaohua, additional, Meyer, Christopher, additional, Thangaraj, Naina, additional, Tater, Pamella, additional, Kandali, Vijay, additional, Ma, Singer, additional, Nguyen, Tuan, additional, Serang, Omar, additional, McGuire, Irina, additional, Robison, Nedra, additional, Gentry, Darrell, additional, Tang, Xing, additional, Palmer, Lance, additional, Wu, Gang, additional, Suh, Ed, additional, Tanner, Leigh, additional, McMurry, James, additional, Lear, Matthew, additional, Wang, Zhaoming, additional, Wilson, Carmen, additional, Cheng, Yong, additional, Weiss, Mitch, additional, Armstrong, Gregory T., additional, Robison, Leslie L., additional, Yasui, Yutaka, additional, Nichols, Kim E., additional, Ellison, David W., additional, Bangur, Chitanya, additional, Mullighan, Charles G., additional, Baker, Suzanne J., additional, Dyer, Michael, additional, Miller, Geralyn, additional, Rusch, Michael, additional, Daly, Richard, additional, Perry, Keith, additional, Downing, James R., additional, and Zhang, Jinghui, additional

Published
2020
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26. Abstract 1198: The St. Jude Survivorship Portal links whole-genome genetic data with clinical therapy and outcome phenotypes for 7302 pediatric cancer survivors

Author

Zhou, Xin, primary, Bhakta, Nickhill, additional, Wang, Jian, additional, Sioson, Edgar, additional, Patel, Jaimin, additional, Shelton, Kyla, additional, Wang, Zhaoming, additional, Lei, Shaohua, additional, Gout, Alexander M., additional, Wilson, Carmen L., additional, Leisenring, Wendy, additional, Bhatia, Smita, additional, Yasui, Yutaka, additional, Hudson, Melissa M., additional, Armstrong, Gregory T., additional, Robison, Leslie L., additional, and Zhang, Jinghui, additional

Published
2020
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28. Polygenic Risk Score Improves Risk Stratification and Prediction of Subsequent Thyroid Cancer after Childhood Cancer.

Author

Nan Song, Qi Liu, Wilson, Carmen L., Sapkota, Yadav, Ehrhardt, Matthew J., Gibson, Todd M., Morton, Lindsay M., Chanock, Stephen J., Neglia, Joseph P., Arnold, Michael A., Michael, J. Robert, Gout, Alexander M., Mulder, Heather L., Easton, John, Bhatia, Smita, Armstrong, Gregory T., Jinghui Zhang, Delaney, Angela, Hudson, Melissa M., and Robison, Leslie L.

Abstract

Background: Subsequent thyroid cancer (STC) is one of the most common malignancies in childhood cancer survivors. We aimed to evaluate the polygenic contributions to STC risk and potential utility in improving risk prediction. Methods: A polygenic risk score (PRS) was calculated from 12 independent SNPs associated with thyroid cancer risk in the general population. Associations between PRS and STC risk were evaluated among survivors from St. Jude Lifetime Cohort (SJLIFE) and were replicated in survivors from Childhood Cancer Survivor Study (CCSS). A risk prediction model integrating the PRS and clinical factors, initially developed in SJLIFE, and its performance were validated in CCSS. Results: Among 2,370 SJLIFE survivors with a median follow-up of 28.8 [interquartile range (IQR) = 21.9-36.1] years, 65 (2.7%) developed STC. Among them, the standardized PRS was associated with an increased rate of STC [relative rate (RR) = 1.57; 95% confidence interval (CI) = 1.24-1.98; P < 0.001]. Similar associations were replicated in 6,416 CCSS survivors, among whom 121 (1.9%) developed STC during median follow-up of 28.9 (IQR = 22.6-34.6) years (RR = 1.52; 95% CI = 1.25-1.83; P < 0.001). A risk prediction model integrating the PRS with clinical factors showed better performance than the model considering only clinical factors in SJLIFE (P = 0.004, AUC = 83.2% vs. 82.1%, at age 40), which was further validated in CCSS (P = 0.010, AUC = 72.9% vs. 70.6%). Conclusions: Integration of the PRS with clinical factors provided a statistically significant improvement in risk prediction of STC, although the magnitude of improvement was modest. Impact: PRS improves risk stratification and prediction of STC, suggesting its potential utility for optimizing screening strategies in survivorship care. [ABSTRACT FROM AUTHOR]

Published
2021
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30. Persistent activation of interlinked type 2 airway epithelial gene networks in sputum-derived cells from aeroallergen-sensitized symptomatic asthmatics

Author

Jones, Anya C., primary, Troy, Niamh M., additional, White, Elisha, additional, Hollams, Elysia M., additional, Gout, Alexander M., additional, Ling, Kak-Ming, additional, Kicic, Anthony, additional, Stick, Stephen M., additional, Sly, Peter D., additional, Holt, Patrick G., additional, Hall, Graham L., additional, and Bosco, Anthony, additional

Published
2018
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32. Persistent activation of interlinked Th2-airway epithelial gene networks in sputum-derived cells from aeroallergen-sensitized symptomatic atopic asthmatics

Author

Jones, Anya C., primary, Troy, Niamh M., additional, White, Elisha, additional, Hollams, Elysia M., additional, Gout, Alexander M., additional, Ling, Kak-Ming, additional, Kicic, Anthony, additional, Sly, Peter D, additional, Holt, Patrick G, additional, Hall, Graham L, additional, and Bosco, Anthony, additional

Published
2016
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33. Systematic chemical and molecular profiling of MLL-rearranged infant acute lymphoblastic leukemia reveals efficacy of romidepsin

Author

Cruickshank, M N, primary, Ford, J, additional, Cheung, L C, additional, Heng, J, additional, Singh, S, additional, Wells, J, additional, Failes, T W, additional, Arndt, G M, additional, Smithers, N, additional, Prinjha, R K, additional, Anderson, D, additional, Carter, K W, additional, Gout, A M, additional, Lassmann, T, additional, O'Reilly, J, additional, Cole, C H, additional, Kotecha, R S, additional, and Kees, U R, additional

Published
2016
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34. Analysis of published PKD1 gene sequence variants

Author

Gout, A. M., ADPKD Gene Variant Consortium, Ravine, D., Harris, P. C., Rossetti, S., Peters, D., Breuning, M., Henske, E. P., Koizumi, A., Inoue, S., Shimizu, Y., Thongnoppakhun, W., Yenchitsomanus, P. T., Deltas, C., Sandford, R., Torra, R., Turco, Alberto, Jeffery, S., Fontes, M., Somlo, S., Furu, L. M., Smulders, Y. M., Mercier, B., Ferec, C., Burtey, S., Pei, Y., Kalaydjieva, L., Bogdanova, N., Mccluskey, M., Geon, L. J., Wouters, C. H., Reiterova, J., Stekrová, J., San Millan, J. L., Aguiari, G., and Del Senno, L.

Subjects
Genetics, sequence variants, Polymorphism, Genetic, TRPP Cation Channels, PKD1, Base Sequence, business.industry, Biology, Text mining, ADPKD, Polymorphism (computer science), Research Design, Humans, Base sequence, Gene sequence, business
Published
2007

35. Analysis of published PKD1 gene sequence variants [3]

Author

Gout, A. M., Ravine, D., Harris, Peter C., Rossetti, S., Peters, D., Breuning, M., Henske, E. P., Koizumi, A., Inoue, S., Shimizu, Y., Thongnoppakhun, W., Yenchitsomanus, P. -T, Constantinou-Deltas, Constantinos D., Sandford, R., Torra, R., Turco, A. E., Jeffery, S., Fontes, M., Somlo, Stefan, Furu, L. M., Smulders, Y. M., Mercier, B., Ferec, C., Burtey, S., Pei, Y., Kalaydjieva, L., Bogdanova, N., McCluskey, M., Geon, L. J., Wouters, C. H., Reiterova, J., Stekrová, J., San Millan, J. L., Aguiari, G., Senno, L. D., and Constantinou-Deltas, Constantinos D. [0000-0001-5549-9169]

Subjects
Polymorphism, Genetic, polycystin 1, TRPP Cation Channels, Base Sequence, gene locus, genotype, letter, nucleotide sequence, gene sequence, genetic analysis, genetic risk, kidney polycystic disease, priority journal, Research Design, data base, computer program, genetic variability, Humans, genetic polymorphism, pathogenicity, human, gene mutation, orthology
Abstract

39 427 428 Cited By :13

Published
2007

37. Subcompartmentalisation of Proteins in the Rhoptries Correlates with Ordered Events of Erythrocyte Invasion by the Blood Stage Malaria Parasite

Author

Zuccala, Elizabeth S., primary, Gout, Alexander M., additional, Dekiwadia, Chaitali, additional, Marapana, Danushka S., additional, Angrisano, Fiona, additional, Turnbull, Lynne, additional, Riglar, David T., additional, Rogers, Kelly L., additional, Whitchurch, Cynthia B., additional, Ralph, Stuart A., additional, Speed, Terence P., additional, and Baum, Jake, additional

Published
2012
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38. TOOWOOMBA DIABETIC SURVEY

Author

smithurst, B. A. and Gout, W. M. G.

Abstract

In 1970, a follow‐up survey was undertaken on diabetics and potential diabetics who were recorded in the 1966 Toowoomba Survey. The project was designed as an exercise in gathering data on community health. Questions were asked on types of treatment, complications and restrictions inactivity and a survival chart was constructed which confirmed the lower expectations of life in diabetics. It was concluded that diabetic patients could, in general, be managed in the community and that such care would be improved by the establishment of community care centres.

Published
1915
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