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1.

Genomic landscape of Down syndrome-associated acute lymphoblastic leukemia.

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; Yang, Jun J.

Blood ; 142(2): 172-184, 2023 07 13.

Article in English | MEDLINE | ID: mdl-37001051

2.

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

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

Genome Res ; 29(9): 1555-1565, 2019 09.

Article in English | MEDLINE | ID: mdl-31439692

3.

RNA-seq Fusion Detection in Clinical Oncology.

Hedges, Dale J.

Adv Exp Med Biol ; 1361: 163-175, 2022.

Article in English | MEDLINE | ID: mdl-35230688

4.

Estimated number of adult survivors of childhood cancer in United States with cancer-predisposing germline variants.

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

Pediatr Blood Cancer ; 67(2): e28047, 2020 02.

Article in English | MEDLINE | ID: mdl-31736278

5.

A comprehensive approach to expression of L1 loci.

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

Nucleic Acids Res ; 45(5): e31, 2017 03 17.

Article in English | MEDLINE | ID: mdl-27899577

6.

The contribution of alu elements to mutagenic DNA double-strand break repair.

Morales, Maria E; White, Travis B; Streva, Vincent A; DeFreece, Cecily B; Hedges, Dale J; Deininger, Prescott L.

PLoS Genet ; 11(3): e1005016, 2015 Mar.

Article in English | MEDLINE | ID: mdl-25761216

7.

Reconstructing the population genetic history of the Caribbean.

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

PLoS Genet ; 9(11): e1003925, 2013 Nov.

Article in English | MEDLINE | ID: mdl-24244192

8.

Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals.

Streva, Vincent A; Jordan, Vallmer E; Linker, Sara; Hedges, Dale J; Batzer, Mark A; Deininger, Prescott L.

BMC Genomics ; 16: 220, 2015 Mar 21.

Article in English | MEDLINE | ID: mdl-25887476

9.

Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion.

Wagstaff, Bradley J; Hedges, Dale J; Derbes, Rebecca S; Campos Sanchez, Rebeca; Chiaromonte, Francesca; Makova, Kateryna D; Roy-Engel, Astrid M.

PLoS Genet ; 8(8): e1002842, 2012.

Article in English | MEDLINE | ID: mdl-22912586

10.

Evaluating mitochondrial DNA variation in autism spectrum disorders.

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; McCauley, Jacob L.

Ann Hum Genet ; 77(1): 9-21, 2013 Jan.

Article in English | MEDLINE | ID: mdl-23130936

11.

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

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; Ross, Mark T.

Leukemia ; 37(3): 518-528, 2023 03.

Article in English | MEDLINE | ID: mdl-36658389

12.

The genomic landscape of pediatric acute lymphoblastic leukemia.

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.

Nat Genet ; 54(9): 1376-1389, 2022 09.

Article in English | MEDLINE | ID: mdl-36050548

13.

Methylation profiling reveals novel molecular classes of rhabdomyosarcoma.

Clay, Michael R; Patel, Anand; Tran, Quynh; Hedges, Dale J; Chang, Ti-Cheng; Stewart, Elizabeth; Charville, Greg; Cline, Cynthia; Dyer, Michael A; Orr, Brent A.

Sci Rep ; 11(1): 22213, 2021 11 15.

Article in English | MEDLINE | ID: mdl-34782706

14.

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

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

Cancer Discov ; 11(12): 3008-3027, 2021 12 01.

Article in English | MEDLINE | ID: mdl-34301788

15.

Primary bone sarcoma with BCOR internal tandem duplication.

Malik, Faizan; Zreik, Riyam T; Hedges, Dale J; Nakitandwe, Joy; Lee, Seungjae; Ward, Russell A; McCarville, M Beth; Pappo, Alberto; Bahrami, Armita.

Virchows Arch ; 476(6): 915-920, 2020 Jun.

Article in English | MEDLINE | ID: mdl-31900635

16.

Rare mutations of FGFR2 causing apert syndrome: identification of the first partial gene deletion, and an Alu element insertion from a new subfamily.

Bochukova, Elena G; Roscioli, Tony; Hedges, Dale J; Taylor, Indira B; Johnson, David; David, David J; Deininger, Prescott L; Wilkie, Andrew O M.

Hum Mutat ; 30(2): 204-11, 2009 Feb.

Article in English | MEDLINE | ID: mdl-18726952

17.

Alu repeats increase local recombination rates.

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

BMC Genomics ; 10: 530, 2009 Nov 16.

Article in English | MEDLINE | ID: mdl-19917129

18.

A genome-wide association study of autism reveals a common novel risk locus at 5p14.1.

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; Pericak-Vance, Margaret A.

Ann Hum Genet ; 73(Pt 3): 263-73, 2009 May.

Article in English | MEDLINE | ID: mdl-19456320

19.

Sample degradation leads to false-positive copy number variation calls in multiplex real-time polymerase chain reaction assays.

Cukier, Holly N; Pericak-Vance, Margaret A; Gilbert, John R; Hedges, Dale J.

Anal Biochem ; 386(2): 288-90, 2009 Mar 15.

Article in English | MEDLINE | ID: mdl-19121619

20.

Identification of repeat structure in large genomes using repeat probability clouds.

Gu, Wanjun; Castoe, Todd A; Hedges, Dale J; Batzer, Mark A; Pollock, David D.

Anal Biochem ; 380(1): 77-83, 2008 Sep 01.

Article in English | MEDLINE | ID: mdl-18541131

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