Search

Your search keyword '"Mulder, Heather"' showing total 300 results
Start Over Author "Mulder, Heather"
300 results on '"Mulder, Heather"'

2. 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

3. Genetic and epigenetic features of bilateral Wilms tumor predisposition in patients from the Children’s Oncology Group AREN18B5-Q

Author

Murphy, Andrew J., Cheng, Changde, Williams, Justin, Shaw, Timothy I., Pinto, Emilia M., Dieseldorff-Jones, Karissa, Brzezinski, Jack, Renfro, Lindsay A., Tornwall, Brett, Huff, Vicki, Hong, Andrew L., Mullen, Elizabeth A., Crompton, Brian, Dome, Jeffrey S., Fernandez, Conrad V., Geller, James I., Ehrlich, Peter F., Mulder, Heather, Oak, Ninad, Maciezsek, Jamie, Jablonowski, Carolyn M., Fleming, Andrew M., Pichavaram, Prahalathan, Morton, Christopher L., Easton, John, Nichols, Kim E., Clay, Michael R., Santiago, Teresa, Zhang, Jinghui, Yang, Jun, Zambetti, Gerard P., Wang, Zhaoming, Davidoff, Andrew M., and Chen, Xiang

Published
2023
Full Text
View/download PDF

4. Distinct DNA methylation signatures associated with blood lipids as exposures or outcomes among survivors of childhood cancer: a report from the St. Jude lifetime cohort

Author

Dong, Qian, Chen, Cheng, Song, Nan, Qin, Na, Plonski, Noel-Marie, Finch, Emily R., Shelton, Kyla, Easton, John, Mulder, Heather, Plyer, Emily, Neale, Geoffrey, Walker, Emily, Li, Qian, Huang, I-Chan, Zhang, Jinghui, Wang, Hui, Hudson, Melissa M., Robison, Leslie L., Ness, Kirsten K., and Wang, Zhaoming

Published
2023
Full Text
View/download PDF

6. Cancer germline predisposing variants and late mortality from subsequent malignant neoplasms among long-term childhood cancer survivors: a report from the St Jude Lifetime Cohort and the Childhood Cancer Survivor Study

Author

Chen, Cheng, Qin, Na, Wang, Mingjuan, Dong, Qian, Tithi, Saima Sultana, Hui, Yawei, Chen, Wenan, Wu, Gang, Kennetz, Dennis, Edmonson, Michael N, Rusch, Michael C, Thrasher, Andrew, Easton, John, Mulder, Heather L, Song, Nan, Plonski, Noel-Marie, Shelton, Kyla, Im, Cindy, Ehrhardt, Matthew J, Nichols, Kim E, Leisenring, Wendy M, Stratton, Kayla L, Howell, Rebecca, Yasui, Yutaka, Bhatia, Smita, Armstrong, Gregory T, Ness, Kirsten K, Hudson, Melissa M, Zhang, Jinghui, Wang, Hui, Srivastava, Deo Kumar, Robison, Leslie L, and Wang, Zhaoming

Published
2023
Full Text
View/download PDF

9. Health-related quality of life and DNA methylation-based aging biomarkers among survivors of childhood cancer.

Author

Plonski, Noel-Marie, Pan, Yue, Chen, Cheng, Dong, Qian, Zhang, Xijun, Song, Nan, Shelton, Kyla, Easton, John, Mulder, Heather, Zhang, Jinghui, Neale, Geoffrey, Walker, Emily, Wang, Hui, Webster, Rachel, Brinkman, Tara, Krull, Kevin R, Armstrong, Gregory T, Ness, Kirsten K, Hudson, Melissa M, and Li, Qian

Subjects
QUALITY of life, CHILDHOOD cancer, CANCER survivors, BIOMARKERS, AGING
Abstract

Background Childhood cancer survivors are at high risk for morbidity and mortality and poor patient-reported outcomes, typically health-related quality of life (HRQOL). However, associations between DNA methylation–based aging biomarkers and HRQOL have not been evaluated. Methods DNA methylation was generated with Infinium EPIC BeadChip on blood-derived DNA (median for age at blood draw = 34.5 years, range = 18.5-66.6 years), and HRQOL was assessed with age at survey (mean = 32.3 years, range = 18.4-64.5 years) from 2206 survivors in the St Jude Lifetime Cohort. DNA methylation–based aging biomarkers, including epigenetic age using multiple clocks (eg, GrimAge) and others (eg, DNAmB2M: beta-2-microglobulin; DNAmADM: adrenomedullin), were derived from the DNAm Age Calculator (https://dnamage.genetics.ucla.edu). HRQOL was assessed using the Medical Outcomes Study 36-Item Short-Form Health Survey to capture 8 domains and physical and mental component summaries. General linear models evaluated associations between HRQOL and epigenetic age acceleration (EAA; eg, EAA_GrimAge) or other age-adjusted DNA methylation–based biomarkers (eg, ageadj_DNAmB2M) after adjusting for age at blood draw, sex, cancer treatments, and DNA methylation–based surrogate for smoking pack-years. All P values were 2-sided. Results Worse HRQOL was associated with greater EAA_GrimAge (physical component summaries: β = -0.18 years, 95% confidence interval [CI] = -0.251 to -0.11 years; P  = 1.85 × 10−5; and 4 individual HRQOL domains), followed by ageadj_DNAmB2M (physical component summaries: β = -0.08 years, 95% CI = -0.124 to -0.037 years; P  = .003; and 3 individual HRQOL domains) and ageadj_DNAmADM (physical component summaries: β = -0.082 years, 95% CI = -0.125 to -0.039 years; P  = .002; and 2 HRQOL domains). EAA_Hannum (Hannum clock) was not associated with any HRQOL. Conclusions Overall and domain-specific measures of HRQOL are associated with DNA methylation measures of biological aging. Future longitudinal studies should test biological aging as a potential mechanism underlying the association between poor HRQOL and increased risk of clinically assessed adverse health outcomes. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

11. A polygenic score for acute vaso-occlusive pain in pediatric sickle cell disease

Author

Rampersaud, Evadnie, Kang, Guolian, Palmer, Lance E., Rashkin, Sara R., Wang, Shuoguo, Bi, Wenjian, Alberts, Nicole M., Anghelescu, Doralina, Barton, Martha, Birch, Kirby, Boulos, Nidal, Brandow, Amanda M., Brooke, Russell John, Chang, Ti-Cheng, Chen, Wenan, Cheng, Yong, Ding, Juan, Easton, John, Hodges, Jason R., Kanne, Celeste K., Levy, Shawn, Mulder, Heather, Patel, Ashwin P., Puri, Latika, Rosencrance, Celeste, Rusch, Michael, Sapkota, Yadav, Sioson, Edgar, Sharma, Akshay, Tang, Xing, Thrasher, Andrew, Wang, Winfred, Yao, Yu, Yasui, Yutaka, Yergeau, Donald, Hankins, Jane S., Sheehan, Vivien A., Downing, James R., Estepp, Jeremie H., Zhang, Jinghui, DeBaun, Michael, Wu, Gang, and Weiss, Mitchell J.

Published
2021
Full Text
View/download PDF

12. Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology

Author

Qaddoumi, Ibrahim, Orisme, Wilda, Wen, Ji, Santiago, Teresa, Gupta, Kirti, Dalton, James D, Tang, Bo, Haupfear, Kelly, Punchihewa, Chandanamali, Easton, John, Mulder, Heather, Boggs, Kristy, Shao, Ying, Rusch, Michael, Becksfort, Jared, Gupta, Pankaj, Wang, Shuoguo, Lee, Ryan P, Brat, Daniel, Peter Collins, V, Dahiya, Sonika, George, David, Konomos, William, Kurian, Kathreena M, McFadden, Kathryn, Serafini, Luciano Neder, Nickols, Hilary, Perry, Arie, Shurtleff, Sheila, Gajjar, Amar, Boop, Fredrick A, Klimo, Paul D, Mardis, Elaine R, Wilson, Richard K, Baker, Suzanne J, Zhang, Jinghui, Wu, Gang, Downing, James R, Tatevossian, Ruth G, and Ellison, David W

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Genetics, Brain Cancer, Biotechnology, Brain Disorders, Rare Diseases, Neurosciences, Cancer, Adolescent, Adult, Astrocytoma, Brain Neoplasms, Child, Child, Preschool, DNA-Binding Proteins, Female, Ganglioglioma, Genes, myb, Genetic Predisposition to Disease, Glioma, Humans, Infant, Male, Mutation, Nuclear Proteins, Nucleocytoplasmic Transport Proteins, Proto-Oncogene Proteins, Proto-Oncogene Proteins B-raf, RNA-Binding Proteins, Receptor, Fibroblast Growth Factor, Type 1, Trans-Activators, Transcription Factors, Young Adult, Glioneuronal, RNA-seq, FGFR1, MYB, BRAF, Neurology & Neurosurgery
Abstract

Low-grade neuroepithelial tumors (LGNTs) are diverse CNS tumors presenting in children and young adults, often with a history of epilepsy. While the genetic profiles of common LGNTs, such as the pilocytic astrocytoma and 'adult-type' diffuse gliomas, are largely established, those of uncommon LGNTs remain to be defined. In this study, we have used massively parallel sequencing and various targeted molecular genetic approaches to study alterations in 91 LGNTs, mostly from children but including young adult patients. These tumors comprise dysembryoplastic neuroepithelial tumors (DNETs; n = 22), diffuse oligodendroglial tumors (d-OTs; n = 20), diffuse astrocytomas (DAs; n = 17), angiocentric gliomas (n = 15), and gangliogliomas (n = 17). Most LGNTs (84 %) analyzed by whole-genome sequencing (WGS) were characterized by a single driver genetic alteration. Alterations of FGFR1 occurred frequently in LGNTs composed of oligodendrocyte-like cells, being present in 82 % of DNETs and 40 % of d-OTs. In contrast, a MYB-QKI fusion characterized almost all angiocentric gliomas (87 %), and MYB fusion genes were the most common genetic alteration in DAs (41 %). A BRAF:p.V600E mutation was present in 35 % of gangliogliomas and 18 % of DAs. Pathogenic alterations in FGFR1/2/3, BRAF, or MYB/MYBL1 occurred in 78 % of the series. Adult-type d-OTs with an IDH1/2 mutation occurred in four adolescents, the youngest aged 15 years at biopsy. Despite a detailed analysis, novel genetic alterations were limited to two fusion genes, EWSR1-PATZ1 and SLMAP-NTRK2, both in gangliogliomas. Alterations in BRAF, FGFR1, or MYB account for most pathogenic alterations in LGNTs, including pilocytic astrocytomas, and alignment of these genetic alterations and cytologic features across LGNTs has diagnostic implications. Additionally, therapeutic options based upon targeting the effects of these alterations are already in clinical trials.

Published
2016

13. SJPedPanel: A pan-cancer gene panel for childhood malignancies

Author

Kolekar, Pandurang, primary, Balagopal, Vidya, additional, Dong, Li, additional, Liu, Yanling, additional, Foy, Scott, additional, Tran, Quang, additional, Mulder, Heather, additional, Huskey, Anna LW, additional, Plyler, Emily, additional, Liang, Zhikai, additional, Ma, Jingqun, additional, Nakitandwe, Joy, additional, Gu, Jiali, additional, Maciaszek, Jamie, additional, Payne-Turner, Debbie, additional, Mallampati, Saradhi, additional, Wang, Lu, additional, Stewart, Elizabeth, additional, Easton, John, additional, Klco, Jeffery M, additional, and Ma, Xiaotu, additional

Published
2023
Full Text
View/download PDF

15. Persistent variations of blood DNA methylation associated with treatment exposures and risk for cardiometabolic outcomes in long-term survivors of childhood cancer in the St. Jude Lifetime Cohort

Author

Song, Nan, Hsu, Chia-Wei, Pan, Haitao, Zheng, Yinan, Hou, Lifang, Sim, Jin-ah, Li, Zhenghong, Mulder, Heather, Easton, John, Walker, Emily, Neale, Geoffrey, Wilson, Carmen L., Ness, Kirsten K., Krull, Kevin R., Srivastava, Deo Kumar, Yasui, Yutaka, Zhang, Jinghui, Hudson, Melissa M., Robison, Leslie L., Huang, I-Chan, and Wang, Zhaoming

Published
2021
Full Text
View/download PDF

17. 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
Full Text
View/download PDF

18. Epigenetic Age in Peripheral Blood Among Children, Adolescent, and Adult Survivors of Childhood Cancer

Author

Plonski, Noel-Marie, primary, Chen, Cheng, additional, Dong, Qian, additional, Qin, Na, additional, Song, Nan, additional, Parikh, Hemang M., additional, Shelton, Kyla, additional, Finch, Emily R., additional, Easton, John, additional, Mulder, Heather, additional, Zhang, Jinghui, additional, Neale, Geoffrey, additional, Walker, Emily, additional, Wang, Hui, additional, Krull, Kevin, additional, Ness, Kirsten K., additional, Hudson, Melissa M., additional, Robison, Leslie L., additional, Li, Qian, additional, Williams, AnnaLynn, additional, and Wang, Zhaoming, additional

Published
2023
Full Text
View/download PDF

19. Abstract LB077: Analysis of indel and structural variant error profiles in deep next generation sequencing data

Author

Shao, Ying, primary, Tran, Quang, additional, Kolekar, Pandurang, additional, Liu, Yanling, additional, McBride, Andrea, additional, Jones, Tyler, additional, Mulder, Heather, additional, Ji, Lingyun, additional, Huang, Benjamin, additional, Meshinchi, Soheil, additional, Klco, Jeffery, additional, Zhang, Jinghui, additional, Carroll, William, additional, Loh, Mignon, additional, Brown, Patrick, additional, Easton, John, additional, and Ma, Xiaotu, additional

Published
2023
Full Text
View/download PDF

20. Supplementary Excel Tables from Integrative Genomic Analysis of Pediatric Myeloid-Related Acute Leukemias Identifies Novel Subtypes and Prognostic Indicators

Author

Fornerod, Maarten, primary, Ma, Jing, primary, Noort, Sanne, primary, Liu, Yu, primary, Walsh, Michael P., primary, Shi, Lei, primary, Nance, Stephanie, primary, Liu, Yanling, primary, Wang, Yuanyuan, primary, Song, Guangchun, primary, Lamprecht, Tamara, primary, Easton, John, primary, Mulder, Heather L., primary, Yergeau, Donald, primary, Myers, Jacquelyn, primary, Kamens, Jennifer L., primary, Obeng, Esther A., primary, Pigazzi, Martina, primary, Jarosova, Marie, primary, Kelaidi, Charikleia, primary, Polychronopoulou, Sophia, primary, Lamba, Jatinder K., primary, Baker, Sharyn D., primary, Rubnitz, Jeffrey E., primary, Reinhardt, Dirk, primary, van den Heuvel-Eibrink, Marry M., primary, Locatelli, Franco, primary, Hasle, Henrik, primary, Klco, Jeffery M., primary, Downing, James R., primary, Zhang, Jinghui, primary, Pounds, Stanley, primary, Zwaan, C. Michel, primary, and Gruber, Tanja A., primary

Published
2023
Full Text
View/download PDF

21. Supplementary Tables and Figures from Integrative Genomic Analysis of Pediatric Myeloid-Related Acute Leukemias Identifies Novel Subtypes and Prognostic Indicators

Author

Fornerod, Maarten, primary, Ma, Jing, primary, Noort, Sanne, primary, Liu, Yu, primary, Walsh, Michael P., primary, Shi, Lei, primary, Nance, Stephanie, primary, Liu, Yanling, primary, Wang, Yuanyuan, primary, Song, Guangchun, primary, Lamprecht, Tamara, primary, Easton, John, primary, Mulder, Heather L., primary, Yergeau, Donald, primary, Myers, Jacquelyn, primary, Kamens, Jennifer L., primary, Obeng, Esther A., primary, Pigazzi, Martina, primary, Jarosova, Marie, primary, Kelaidi, Charikleia, primary, Polychronopoulou, Sophia, primary, Lamba, Jatinder K., primary, Baker, Sharyn D., primary, Rubnitz, Jeffrey E., primary, Reinhardt, Dirk, primary, van den Heuvel-Eibrink, Marry M., primary, Locatelli, Franco, primary, Hasle, Henrik, primary, Klco, Jeffery M., primary, Downing, James R., primary, Zhang, Jinghui, primary, Pounds, Stanley, primary, Zwaan, C. Michel, primary, and Gruber, Tanja A., primary

Published
2023
Full Text
View/download PDF

22. Figures S1-S10 and Tables S1, S3-S6 from Dynamics of Age- versus Therapy-Related Clonal Hematopoiesis in Long-term Survivors of Pediatric Cancer

Author

Hagiwara, Kohei, primary, Natarajan, Sivaraman, primary, Wang, Zhaoming, primary, Zubair, Haseeb, primary, Mulder, Heather L., primary, Dong, Li, primary, Plyler, Emily M., primary, Thimmaiah, Padma, primary, Ma, Xiaotu, primary, Ness, Kristen K., primary, Li, Zhenghong, primary, Mulrooney, Daniel A., primary, Wilson, Carmen L., primary, Yasui, Yutaka, primary, Hudson, Melissa M., primary, Easton, John, primary, Robison, Leslie L., primary, and Zhang, Jinghui, primary

Published
2023
Full Text
View/download PDF

23. Abstract 4363: Monocyte-specific epigenetic age acceleration and cardiomyopathy risk among survivors of childhood cancer

Author

Chen, Cheng, primary, Dong, Qian, additional, Na, Qin, additional, Song, Nan, additional, Easton, John, additional, Mulder, Heather L., additional, Walker, Emily, additional, Neale, Geoffrey, additional, Finch, Emily R., additional, Li, Qian, additional, Yasui, Yutaka, additional, Mulrooney, Daniel A., additional, Hudson, Melissa M., additional, Ness, Kirsten K., additional, Zhang, Jinghui, additional, Chen, Xiang, additional, Wang, Hui, additional, Robison, Leslie L., additional, and Wang, Zhaoming, additional

Published
2023
Full Text
View/download PDF

24. Abstract 4514: Variations of blood DNA methylation associated with cancer treatment exposures among childhood cancer survivors of African ancestry

Author

Dong, Qian, primary, Das, Sarmistha, additional, Chen, Cheng, additional, Easton, John, additional, Mulder, Heather L., additional, Walker, Emily, additional, Neale, Geoffrey, additional, Srivastava, Deo Kumar, additional, Huang, I-Chan, additional, Zhang, Jinghui, additional, Hudson, Melissa M., additional, Robison, Leslie L., additional, Ness, Kirsten K., additional, Song, Nan, additional, and Wang, Zhaoming, additional

Published
2023
Full Text
View/download PDF

25. Data from Integrative Genomic Analysis of Pediatric Myeloid-Related Acute Leukemias Identifies Novel Subtypes and Prognostic Indicators

Author

Fornerod, Maarten, primary, Ma, Jing, primary, Noort, Sanne, primary, Liu, Yu, primary, Walsh, Michael P., primary, Shi, Lei, primary, Nance, Stephanie, primary, Liu, Yanling, primary, Wang, Yuanyuan, primary, Song, Guangchun, primary, Lamprecht, Tamara, primary, Easton, John, primary, Mulder, Heather L., primary, Yergeau, Donald, primary, Myers, Jacquelyn, primary, Kamens, Jennifer L., primary, Obeng, Esther A., primary, Pigazzi, Martina, primary, Jarosova, Marie, primary, Kelaidi, Charikleia, primary, Polychronopoulou, Sophia, primary, Lamba, Jatinder K., primary, Baker, Sharyn D., primary, Rubnitz, Jeffrey E., primary, Reinhardt, Dirk, primary, van den Heuvel-Eibrink, Marry M., primary, Locatelli, Franco, primary, Hasle, Henrik, primary, Klco, Jeffery M., primary, Downing, James R., primary, Zhang, Jinghui, primary, Pounds, Stanley, primary, Zwaan, C. Michel, primary, and Gruber, Tanja A., primary

Published
2023
Full Text
View/download PDF

26. Abstract 3503: Racial disparity and roles of social determinants of health in epigenetic age acceleration among survivors of childhood cancer

Author

Plonski, Noel-Marie, primary, Chen, Cheng, additional, Dong, Qian, additional, Qin, Na, additional, Song, Nan, additional, Easton, John, additional, Mulder, Heather, additional, Walker, Emily, additional, Neale, Geoffrey, additional, Zhang, Jinghui, additional, Krull, Kevin, additional, Ness, Kirsten K., additional, Hudson, Melissa M., additional, Robison, Leslie L., additional, Huang, I-Chan, additional, and Wang, Zhaoming, additional

Published
2023
Full Text
View/download PDF

27. Tables S2, S7, S8, S9 from Dynamics of Age- versus Therapy-Related Clonal Hematopoiesis in Long-term Survivors of Pediatric Cancer

Author

Hagiwara, Kohei, primary, Natarajan, Sivaraman, primary, Wang, Zhaoming, primary, Zubair, Haseeb, primary, Mulder, Heather L., primary, Dong, Li, primary, Plyler, Emily M., primary, Thimmaiah, Padma, primary, Ma, Xiaotu, primary, Ness, Kristen K., primary, Li, Zhenghong, primary, Mulrooney, Daniel A., primary, Wilson, Carmen L., primary, Yasui, Yutaka, primary, Hudson, Melissa M., primary, Easton, John, primary, Robison, Leslie L., primary, and Zhang, Jinghui, primary

Published
2023
Full Text
View/download PDF

28. Data from Dynamics of Age- versus Therapy-Related Clonal Hematopoiesis in Long-term Survivors of Pediatric Cancer

Author

Hagiwara, Kohei, primary, Natarajan, Sivaraman, primary, Wang, Zhaoming, primary, Zubair, Haseeb, primary, Mulder, Heather L., primary, Dong, Li, primary, Plyler, Emily M., primary, Thimmaiah, Padma, primary, Ma, Xiaotu, primary, Ness, Kristen K., primary, Li, Zhenghong, primary, Mulrooney, Daniel A., primary, Wilson, Carmen L., primary, Yasui, Yutaka, primary, Hudson, Melissa M., primary, Easton, John, primary, Robison, Leslie L., primary, and Zhang, Jinghui, primary

Published
2023
Full Text
View/download PDF

29. Supplementary Tables S1-S5 from The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment

Author

Brady, Samuel W., primary, Ma, Xiaotu, primary, Bahrami, Armita, primary, Satas, Gryte, primary, Wu, Gang, primary, Newman, Scott, primary, Rusch, Michael, primary, Putnam, Daniel K., primary, Mulder, Heather L., primary, Yergeau, Donald A., primary, Edmonson, Michael N., primary, Easton, John, primary, Alexandrov, Ludmil B., primary, Chen, Xiang, primary, Mardis, Elaine R., primary, Wilson, Richard K., primary, Downing, James R., primary, Pappo, Alberto S., primary, Raphael, Benjamin J., primary, Dyer, Michael A., primary, and Zhang, Jinghui, primary

Published
2023
Full Text
View/download PDF

30. Supplementary Figures S1-S11 from The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment

Author

Brady, Samuel W., primary, Ma, Xiaotu, primary, Bahrami, Armita, primary, Satas, Gryte, primary, Wu, Gang, primary, Newman, Scott, primary, Rusch, Michael, primary, Putnam, Daniel K., primary, Mulder, Heather L., primary, Yergeau, Donald A., primary, Edmonson, Michael N., primary, Easton, John, primary, Alexandrov, Ludmil B., primary, Chen, Xiang, primary, Mardis, Elaine R., primary, Wilson, Richard K., primary, Downing, James R., primary, Pappo, Alberto S., primary, Raphael, Benjamin J., primary, Dyer, Michael A., primary, and Zhang, Jinghui, primary

Published
2023
Full Text
View/download PDF

31. Data from The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment

Author

Brady, Samuel W., primary, Ma, Xiaotu, primary, Bahrami, Armita, primary, Satas, Gryte, primary, Wu, Gang, primary, Newman, Scott, primary, Rusch, Michael, primary, Putnam, Daniel K., primary, Mulder, Heather L., primary, Yergeau, Donald A., primary, Edmonson, Michael N., primary, Easton, John, primary, Alexandrov, Ludmil B., primary, Chen, Xiang, primary, Mardis, Elaine R., primary, Wilson, Richard K., primary, Downing, James R., primary, Pappo, Alberto S., primary, Raphael, Benjamin J., primary, Dyer, Michael A., primary, and Zhang, Jinghui, primary

Published
2023
Full Text
View/download PDF

32. MYCN amplification and ATRX mutations are incompatible in neuroblastoma

Author

Zeineldin, Maged, Federico, Sara, Chen, Xiang, Fan, Yiping, Xu, Beisi, Stewart, Elizabeth, Zhou, Xin, Jeon, Jongrye, Griffiths, Lyra, Nguyen, Rosa, Norrie, Jackie, Easton, John, Mulder, Heather, Yergeau, Donald, Liu, Yanling, Wu, Jianrong, Van Ryn, Collin, Naranjo, Arlene, Hogarty, Michael D., Kamiński, Marcin M., Valentine, Marc, Pruett-Miller, Shondra M., Pappo, Alberto, Zhang, Jinghui, Clay, Michael R., Bahrami, Armita, Vogel, Peter, Lee, Seungjae, Shelat, Anang, Sarthy, Jay F., Meers, Michael P., George, Rani E., Mardis, Elaine R., Wilson, Richard K., Henikoff, Steven, Downing, James R., and Dyer, Michael A.

Published
2020
Full Text
View/download PDF

33. Forty-five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor

Author

Murphy, Andrew J., Chen, Xiang, Pinto, Emilia M., Williams, Justin S., Clay, Michael R., Pounds, Stanley B., Cao, Xueyuan, Shi, Lei, Lin, Tong, Neale, Geoffrey, Morton, Christopher L., Woolard, Mary A., Mulder, Heather L., Gil, Hyea Jin, Rehg, Jerold E., Billups, Catherine A., Harlow, Matthew L., Dome, Jeffrey S., Houghton, Peter J., Easton, John, Zhang, Jinghui, George, Rani E., Zambetti, Gerard P., and Davidoff, Andrew M.

Published
2019
Full Text
View/download PDF

34. Supplemental Legend from Shortened Leukocyte Telomere Length Associates with an Increased Prevalence of Chronic Health Conditions among Survivors of Childhood Cancer: A Report from the St. Jude Lifetime Cohort

Author

Song, Nan, primary, Li, Zhenghong, primary, Qin, Na, primary, Howell, Carrie R., primary, Wilson, Carmen L., primary, Easton, John, primary, Mulder, Heather L., primary, Edmonson, Michael N., primary, Rusch, Michael C., primary, Zhang, Jinghui, primary, Hudson, Melissa M., primary, Yasui, Yutaka, primary, Robison, Leslie L., primary, Ness, Kirsten K., primary, and Wang, Zhaoming, primary

Published
2023
Full Text
View/download PDF

35. Supplementary Online Content from Polygenic Determinants for Subsequent Breast Cancer Risk in Survivors of Childhood Cancer: The St Jude Lifetime Cohort Study (SJLIFE)

Author

Wang, Zhaoming, primary, Liu, Qi, primary, Wilson, Carmen L., primary, Easton, John, primary, Mulder, Heather, primary, Chang, Ti-Cheng, primary, Rusch, Michael C., primary, Edmonson, Michael N., primary, Rice, Stephen V., primary, Ehrhardt, Matthew J., primary, Howell, Rebecca M., primary, Kesserwan, Chimene A., primary, Wu, Gang, primary, Nichols, Kim E., primary, Downing, James R., primary, Hudson, Melissa M., primary, Zhang, Jinghui, primary, Yasui, Yutaka, primary, and Robison, Leslie L., primary

Published
2023
Full Text
View/download PDF

36. Data from Shortened Leukocyte Telomere Length Associates with an Increased Prevalence of Chronic Health Conditions among Survivors of Childhood Cancer: A Report from the St. Jude Lifetime Cohort

Author

Song, Nan, primary, Li, Zhenghong, primary, Qin, Na, primary, Howell, Carrie R., primary, Wilson, Carmen L., primary, Easton, John, primary, Mulder, Heather L., primary, Edmonson, Michael N., primary, Rusch, Michael C., primary, Zhang, Jinghui, primary, Hudson, Melissa M., primary, Yasui, Yutaka, primary, Robison, Leslie L., primary, Ness, Kirsten K., primary, and Wang, Zhaoming, primary

Published
2023
Full Text
View/download PDF

37. Supplementary Data from Shortened Leukocyte Telomere Length Associates with an Increased Prevalence of Chronic Health Conditions among Survivors of Childhood Cancer: A Report from the St. Jude Lifetime Cohort

Author

Song, Nan, primary, Li, Zhenghong, primary, Qin, Na, primary, Howell, Carrie R., primary, Wilson, Carmen L., primary, Easton, John, primary, Mulder, Heather L., primary, Edmonson, Michael N., primary, Rusch, Michael C., primary, Zhang, Jinghui, primary, Hudson, Melissa M., primary, Yasui, Yutaka, primary, Robison, Leslie L., primary, Ness, Kirsten K., primary, and Wang, Zhaoming, primary

Published
2023
Full Text
View/download PDF

38. The Genetic and Epigenetic Features of Bilateral Wilms Tumor Predisposition: A Report from the Children's Oncology Group AREN18B5-Q Study

Author

Murphy, Andrew J., primary, Cheng, Changde, additional, Williams, Justin, additional, Shaw, Timothy I., additional, Pinto, Emilia M., additional, Dieseldorff-Jones, Karissa, additional, Brzezinski, Jack, additional, Renfro, Lindsay A., additional, Tornwall, Brett, additional, Huff, Vicki, additional, Hong, Andrew L., additional, Mullen, Elizabeth A., additional, Crompton, Brian, additional, Dome, Jeffrey S., additional, Fernandez, Conrad V., additional, Geller, James I., additional, Ehrlich, Peter F., additional, Mulder, Heather, additional, Oak, Ninad, additional, Maciezsek, Jamie, additional, Jablonowski, Carolyn, additional, Fleming, Andrew M., additional, Pichavaram, Prahalathan, additional, Morton, Christopher L., additional, Easton, John, additional, Nichols, Kim E., additional, Clay, Michael R., additional, Santiago, Teresa, additional, Zhang, Jinghui, additional, Yang, Jun, additional, Zambetti, Gerard P., additional, Wang, Zhaoming, additional, Davidoff, Andrew M., additional, and Chen, Xiang, additional

Published
2023
Full Text
View/download PDF

39. Dynamics of Age- versus Therapy-Related Clonal Hematopoiesis in Long-term Survivors of Pediatric Cancer

Author

Hagiwara, Kohei, primary, Natarajan, Sivaraman, additional, Wang, Zhaoming, additional, Zubair, Haseeb, additional, Mulder, Heather L., additional, Dong, Li, additional, Plyler, Emily M., additional, Thimmaiah, Padma, additional, Ma, Xiaotu, additional, Ness, Kristen K., additional, Li, Zhenghong, additional, Mulrooney, Daniel A., additional, Wilson, Carmen L., additional, Yasui, Yutaka, additional, Hudson, Melissa M., additional, Easton, John, additional, Robison, Leslie L., additional, and Zhang, Jinghui, additional

Published
2023
Full Text
View/download PDF

40. Abstract B017: Epigenetic age in peripheral blood among children, adolescent, and adult survivors of childhood cancer

Author

Plonski, Noel-Marie, primary, Chen, Cheng, additional, Dong, Qian, additional, Qin, Na, additional, Shelton, Kyla C., additional, Finch, Emily, additional, Easton, John, additional, Mulder, Heather, additional, Zhang, Jinghui, additional, Neale, Geoffrey, additional, Walker, Emily, additional, Wang, Hui, additional, Krull, Kevin, additional, Ness, Kirsten K., additional, Hudson, Melissa M, additional, Robinson, Leslie L., additional, Li, Qian, additional, Williams, AnnaLynn, additional, and Wang, Zhaoming, additional

Published
2023
Full Text
View/download PDF

41. Additional file 1 of NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization

Author

Narang, Sonali, Evensen, Nikki A., Saliba, Jason, Pierro, Joanna, Loh, Mignon L., Brown, Patrick A., Kolekar, Pandurang, Mulder, Heather, Shao, Ying, Easton, John, Ma, Xiaotu, Tsirigos, Aristotelis, and Carroll, William L.

Abstract

Additional file 1: Figure S1a. Hi-C million read counts (left) and read percentage (right) per cell line. Figure S2a. Venn diagram showing overlap of differentially expressed genes (abs(L2FC) > 0.32, p-value < 0.05) between three B-ALL cell lines upon knockdown, decreased and increased genes (left and right respectively). b. Volcano plots demonstrating differentially expressed genes (abs(L2FC) > 0.32, p-value < 0.05) highlighted by compartment switch or shift (A to more A, B to A, B to less B, or stable). c. Scatterplot demonstrating compartments colored by concordance score (percentage of genes with that compartment switch or shift that change in the same direction). Figure S3a. Rate of concordance calculations represent the amount of upregulated and downregulated genes (abs(L2FC) > 0.32, p-value < 0.05) that can be explained by compartment switches and shifts. Figure S4a. Barplot showing number of subcompartment calls with SNIPER for each cell line at NSD2 Low and NSD2 High. b. Barplots presenting fraction of Cscore compartment calls (A or B) overlapping SNIPER subcompartment calls (A1, A2, B1, B2, and B3) c. Barplot showing number of subcompartment calls with SNIPER for each cell line at NSD2 Low and NSD2 High excluding B1 subcompartment calls. d. Barplot presenting number of subcompartment switches from A to B and from B to A from NS2D Low to NSD2 High in each of the cell lines. e. Barplots presenting fraction of SNIPER subcompartment calls overlapping cscore compartment switches and shifts. Figure S5a. Correlation boxplots of SNIPER subcompartments and gene expression changes (abs(L2FC) > 0.32, p-value 0.05) for each cell line from NSD2 Low to NSD2 High. b. Volcano plots demonstrate differentially expressed genes (abs(L2FC) > 0.32, p-value < 0.05) highlighted by subcompartment switches and shifts. Figure S6a. PCA of ATAC-seq peaks for each cell line identifies three distinct clusters which are cell line-specific. b. Heat map representation of ATAC-seq results generated with DiffBind. c. Venn Diagram showing overlap of differentially accessible regions between three B-ALL cell lines decreased and increased accessibility (left and right respectively; (FDR < 0.01, abs(log2(fold change)) > 1). d. Example of B to A compartment shift shared by all three cell lines at the NEO1 locus showing concordance with gene expression and chromatin accessibility. e. Example of B to A compartment shift specific to RS4;11 cell line at the PRDM8 locus showing concordance with gene expression and chromatin accessibility. Figure S7a. Heatmap representation of mean intra-TAD activity per cell line. b. Bar plot showing number of TAD activity changes per cell line (abs(L2FC) > 0.25, FDR < 0.01). c. Venn diagrams demonstrating significant overlap of patient NSD2-High upregulated genes and cell line NSD2-High upregulated genes and insignificant overlap of patient NSD2-High downregulated genes and cell line NSD2-High upregulated genes (one-tailed Fisher’s exact test). The last row presents insignificant overlap of genes upregulated in 9 matched D/R patient pairs with no NSD2 mutation (NSD2 Low) and cell line NSD2-High upregulated genes with a B to A compartment switch or shift. d. Table presenting percentage of patient NSD2-High upregulated genes overlapping a compartment switch/shift from any of the three cell lines. Figure S8a. Table presents patient information associated with the three matched diagnosis-relapse pairs acquired from COG. Figure S9a. Rate of concordance calculations present the number of genes upregulated in expression, increased in H3K36me2 ChIP-seq peaks, and B to A compartment shifts and switches for the RCH, RS4;11, and SEM cell lines. b. Association bar plots showing fraction of differential H3K36me2 chip-seq peaks (decreased, increased, and stable) that overlap changes in intra-TAD activity (increased, decreased, and stable TADs).

Published
2023
Full Text
View/download PDF

42. Additional file 1 of Distinct DNA methylation signatures associated with blood lipids as exposures or outcomes among survivors of childhood cancer: a report from the St. Jude lifetime cohort

Author

Dong, Qian, Chen, Cheng, Song, Nan, Qin, Na, Plonski, Noel-Marie, Finch, Emily R., Shelton, Kyla, Easton, John, Mulder, Heather, Plyer, Emily, Neale, Geoffrey, Walker, Emily, Li, Qian, Huang, I-Chan, Zhang, Jinghui, Wang, Hui, Hudson, Melissa M., Robison, Leslie L., Ness, Kirsten K., and Wang, Zhaoming

Abstract

Additional file 1. Supplementary Information.

Published
2023
Full Text
View/download PDF

43. Analysis of error profiles in deep next-generation sequencing data

Author

Ma, Xiaotu, Shao, Ying, Tian, Liqing, Flasch, Diane A., Mulder, Heather L., Edmonson, Michael N., Liu, Yu, Chen, Xiang, Newman, Scott, Nakitandwe, Joy, Li, Yongjin, Li, Benshang, Shen, Shuhong, Wang, Zhaoming, Shurtleff, Sheila, Robison, Leslie L., Levy, Shawn, Easton, John, and Zhang, Jinghui

Published
2019
Full Text
View/download PDF

45. Social‐epigenetic mediators for racial disparities in pulmonary impairment among childhood cancer survivors

Author

Song, Nan, primary, Dong, Qian, additional, Chen, Cheng, additional, Li, Qian, additional, Mulder, Heather, additional, Plyler, Emily, additional, Easton, John, additional, Walker, Emily, additional, Olson, Scott, additional, Neale, Geoffrey, additional, Krull, Kevin R., additional, Srivastava, Deo Kumar, additional, Ness, Kirsten K., additional, Zhang, Jinghui, additional, Hudson, Melissa M., additional, Robison, Leslie L., additional, Huang, I‐Chan, additional, and Wang, Zhaoming, additional

Published
2022
Full Text
View/download PDF

46. Association of Single-Nucleotide Variants in the Human Leukocyte Antigen and Other Loci With Childhood Hodgkin Lymphoma

Author

Chen, Cheng, primary, Song, Nan, additional, Dong, Qian, additional, Sun, Xiaojun, additional, Mulder, Heather L., additional, Easton, John, additional, Zhang, Jinghui, additional, Yasui, Yutaka, additional, Bhatia, Smita, additional, Armstrong, Gregory T., additional, Wang, Hui, additional, Ness, Kirsten K., additional, Hudson, Melissa M., additional, Robison, Leslie L., additional, and Wang, Zhaoming, additional

Published
2022
Full Text
View/download PDF

48. Abstract 499: Accelerated clonal hematopoiesis in survivors of childhood cancer: A report for the St. Jude Lifetime Cohort Study

Author

Hagiwara, Kohei, primary, Wang, Zhaoming, additional, Zubair, Haseeb, additional, Easton, John, additional, Mulder, Heather L., additional, Ma, Xiaotu, additional, Ness, Kristen K., additional, Li, Zhenghong, additional, Mulrooney, Daniel A., additional, Wilson, Carmen L., additional, Yasui, Yutaka, additional, Hudson, Melissa M., additional, Robison, Leslie L., additional, and Zhang, Jinghui, additional

Published
2022
Full Text
View/download PDF

49. Abstract 3764: Epigenome-wide association study of blood lipids among survivors of childhood cancer in the St. Jude Lifetime Cohort

Author

Dong, Qian, primary, Song, Nan, additional, Chen, Cheng, additional, Li, Zhenghong, additional, Easton, John, additional, Mulder, Heather, additional, Zhang, Jinghui, additional, Neale, Geoffrey, additional, Walker, Emily, additional, Huang, I-Chan, additional, Ness, Kirsten K., additional, Hudson, Melissa M., additional, Robison, Leslie L., additional, and Wang, Zhaoming, additional

Published
2022
Full Text
View/download PDF

50. Abstract 6344: HLA and non-HLA associations with childhood and adolescent Hodgkin lymphoma risk

Author

Chen, Cheng, primary, Song, Nan, additional, Sun, Xiaojun, additional, Dong, Qian, additional, Li, Zhenghong, additional, Wang, Hui, additional, Bhatia, Smita, additional, Mulder, Heather, additional, Easton, John, additional, Zhang, Jinghui, additional, Yasui, Yutaka, additional, Armstrong, Gregory T., additional, Ness, Kirsten K., additional, Hudson, Melissa M., additional, Robison, Leslie L., additional, and Wang, Zhaoming, additional

Published
2022
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results