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Dale Hedges, PhD

Dale Hedges, PhD

  • Senior Bioinformatics Research Scientist, Transcriptomics

Education

NIH Postdoctoral Fellow - Tulane Cancer Center, Tulane University
PhD
, Biological Sciences - Louisiana State University, Baton Rouge, LA
BA, Biology, Philosophy - Duke University, Durham, NC

About

Dale Hedges is a senior bioinformatics research scientist within the Transcriptomics Group of the Center for Applied Bioinformatics. Prior to joining St. Jude Children’s Research Hospital, he previously held faculty positions at The Ohio State University and the University of Miami and staff positions at Tulane University and Duke University. His research background includes work in human retrotransposons as well as examining the genetic risk factors contributing to several human diseases, including autism, alzheimer’s and dilated cardiomyopathy. With both wet lab and dry lab backgrounds, Dale's current research interests include developing analysis strategies for emerging genomic technologies.

Research Interests

  • Transcriptomics, including single cell transcription
  • Retrotransposon evolution, biology, and impacts
  • Germline predisposition to human disease

Selected Publications

Malik F, Zreik RT, Hedges DJ, Nakitandwe J, Lee S, Ward RA, McCarville B, Pappo A, Bahrami A. Primary Bone Sarcoma with BCOR Internal Tandem Duplication. Virchows Archiv. 2020 Jan 3, Epub ahead of print, PMID:31900635

Edmonson MN, Patel AN, Hedges DJ, Wang Z, Rampersaud E, Kesserwan CA, Zhou X, Liu Y, Newman S, Rusch MC, McLeod CL, Wilkinson MR, Rice SV, Soussi T, Taylor JP, Benatar M, Becksfort JB, Nichols KE, Robison LL, Downing JR, Zhang J. Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants. Genome Res. 2019 Sep;29(9):1555-1565. PMID:31439692.

Wilson CL, Wang Z, Liu Q, Ehrhardt MJ, Mostafavi R, Easton J, Mulder H, Hedges DJ, Wang S, Rusch M, Edmonson M, Levy S, Lanctot JQ, Currie K, Lear M, Patel A,Sapkota Y, Brooke RJ, Moon W, Chang TC, Chen W, Kesserwan CA, Wu G, Nichols KE,Hudson MM, Zhang J, Robison LL, Yasui Y. Estimated number of adult survivors ofchildhood cancer in United States with cancerpredisposing germline variants. Pediatr Blood Cancer. 2019 Feb;67(2). PMID: 31736278.

Walsh MF, Ritter DI, Kesserwan C, Sonkin D, Chakravarty D, Chao E, Ghosh R,Kemel Y, Wu G, Lee K, Kulkarni S, Hedges D, Mandelker D, Ceyhan-Birsoy O, Luo M, Drazer M, Zhang L, Offit K, Plon SE. Integrating somatic variant data andbiomarkers for germline variant classification in cancer predisposition genes. Hum Mutat. 2018 Nov;39(11):1542-1552. PMID:30311369.

Wang Z, Wilson CL, Easton J, Thrasher A, Mulder H, Liu Q, Hedges DJ, Wang S, Rusch MC, Edmonson MN, Levy S, Lanctot JQ, Caron E, Shelton K, Currie K, Lear M, Patel A, Rosencrance C, Shao Y, Vadodaria B, Yergeau D, Sapkota Y, Brooke RJ, Moon W, Rampersaud E, Ma X, Chang TC, Rice SV, Pepper C, Zhou X, Chen X, Chen W, Jones A, Boone B, Ehrhardt MJ, Krasin MJ, Howell RM, Phillips NS, Lewis C, Srivastava D, Pui CH, Kesserwan CA, Wu G, Nichols KE, Downing JR, Hudson MM, Yasui Y, Robison LL, Zhang J. Genetic Risk for Subsequent Neoplasms Among LongTerm Survivors of Childhood Cancer. J Clin Oncol. 2018 Jul 10;36(20):2078-2087. PMID: 29847298

Rusch M, Nakitandwe J, Shurtleff S, Newman S, Zhang Z, Edmonson MN, Parker M, Jiao Y, Ma X, Liu Y, Gu J, Walsh MF, Becksfort J, Thrasher A, Li Y, McMurry J, Hedlund E, Patel A, Easton J, Yergeau D, Vadodaria B, Tatevossian RG, Raimondi S, Hedges D, Chen X, Hagiwara K, McGee R, Robinson GW, Klco JM, Gruber TA, Ellison DW, Downing JR, Zhang J. Clinical cancer genomic profiling by three platform sequencing of whole genome, whole exome and transcriptome. Nat Commun. 2018 Sep 27;9(1):3962. PMID: 30262806

Deininger P, Morales ME, White TB, Baddoo M, Hedges DJ, Servant G, Srivastav S, Smither ME, Concha M, DeHaro DL, Flemington EK, Belancio VP. A comprehensive approach to expression of L1 loci. Nucleic Acids Res. 2017 Mar 17;45(5). PMID: 27899577

Zhang J, Walsh MF, Wu G, Edmonson MN, Gruber TA, Easton J, Hedges D, Ma X, Zhou X, Yergeau DA, Wilkinson MR, Vadodaria B, Chen X, McGee RB, Hines-Dowell S, Nuccio R, Quinn E, Shurtleff SA, Rusch M, Patel A, Becksfort JB, Wang S, Weaver MS, Ding L, Mardis ER, Wilson RK, Gajjar A, Ellison DW, Pappo AS, Pui CH, Nichols KE, Downing JR. Germline Mutations in Predisposition Genes in Pediatric Cancer. N. Engl J Med. 2015 Dec 10;373(24):2336-46.

Streva VA, Jordan VE, Linker S, Hedges DJ, Batzer MA, Deininger PL. Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals. BMC Genomics. 2015 16:220. PMID:25887476.

Morales ME, White TB, Streva VA, DeFreece CB, Hedges DJ, Deininger PL. The contribution of alu elements to mutagenic DNA double-strand break repair. PLoS Genet. 11;11(3):e1005016. PMID: 25761216.

Moreno-Estrada A, Gravel S, Zakharia F, McCauley JL, Byrnes JK, Gignoux CR, Ortiz-Tello PA, Martínez RJ, Hedges DJ, Morris RW, Eng C, Sandoval K, Acevedo-Acevedo S, Norman PJ, Layrisse Z, Parham P, Martínez-Cruzado JC, Burchard EG, Cuccaro ML, Martin ER, Bustamante CD. Reconstructing the population genetic history of the Caribbean. PLoS Genet. 2013 Nov: 9(11) PMID: 24244192

Linker, S. Hedges, DJ. Linear Decay of Retrotransposon Antisense Bias is Tissue Specific. PLoS One. 2013 9(1): 10.1371. PMID: 24244495. Corresponding author

Norton N, Li D, Rampersaud E, Morales A, Martin ER, Zuchner S, Guo S, Gonzalez M, Hedges DJ, Robertson PD, Krumm N, Nickerson DA, Hershberger RE; National Heart, Lung, and Blood Institute GO Exome Sequencing Project and the Exome Sequencing Project Family Studies Project Team. Exome sequencing and genome-wide linkage analysis in 17 families illustrate the complex contribution of TTN truncating variants to dilated cardiomyopathy. Circ Cardiovasc Genet. 2013 Apr 6(2):144-53. PMID: 23418287.

McElroy JP, Krupp LB, Johnson BA, McCauley JL, Qi Z, Caillier SJ, Gourraud PA, Yu J, Nathanson L, Belman AL, Hauser SL, Waubant E, Hedges DJ, Oksenberg JR. Copy number variation in pediatric multiple sclerosis. Mult Scler. 2013 Jul;19(8):1014-21. PMID: 23239789.

Lin Z, Wang X, Strong MJ, Concha M, Baddoo M, Xu G, Baribault C, Fewell C, Hulme W, Hedges D, Taylor CM, Flemington EK. Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains. J Virol. 2013 Jan;87(2):1172-82. PMID:23152513.

Hadjixenofontos A, Schmidt MA, Whitehead PL, Konidari I, Hedges DJ, Wright HH, Abramson RK, Menon R, Williams SM, Cuccaro ML, Haines JL, Gilbert JR, Pericak-Vance MA, Martin ER, McCauley JL. Evaluating mitochondrial DNA variation in autism spectrum disorders. Ann Hum Genet. 2013 Jan;77(1):9-21. PMID: 23130936.

Hedges DJ, Hamilton-Nelson KL, Sacharow SJ, Nations L, Beecham GW, Kozhekbaeva ZM, Butler BL, Cukier HN, Whitehead PL, Ma D, Jaworski JM, Nathanson L, Lee JM, Hauser SL, Oksenberg JR, Cuccaro ML, Haines JL, Gilbert JR, Pericak-Vance MA. Evidence of Novel Fine-scale Structural Variation at Autism Spectrum Disorder Candidate Loci. Molecular Autism. 2012 Apr 2;3(1):2. PMID: 22472195. First author

Concha M, Wang X, Cao S, Baddoo M, Fewell C, Lin Z, Hulme W, Hedges D, McBride J, Flemington EK. Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq. J Virol. 2012 Feb;86(3):1458-67. PMID:22090128.

Chung RH, Ma D, Wang K, Hedges DJ, Jaworski JM, Gilbert JR, Cuccaro ML, Wright HH, Abrahamson RK, Konidari I, Whitehead PL, Schellenberg GD, Hakonarson H, Haines JL, PericakVance MA, Martin ER. An X-chromosome-wide association study in autism families identifies TBL1X as a novel autism spectrum disorder candidate gene in males, Mol Autism. 2011 Nov 4;2(1):18. PMID: 22050706.

Hedges DJ, Guettouche T, Yang S, Bademci G, Diaz A, Andersen A, Hulme WF, Linker S, Mehta A, Edwards YJK, Beecham GB, Martin ER, Pericak-Vance MA, Zuchner S, Vance JM, Gilbert JR. Comparison of three targeted enrichment strategies on the SOLiD sequencing platform. PloS One. 2011 Apr 29;6(4). PMID: 21559511. First author

Xu G, Fewell C, Taylor C, Deng N, Hedges D, Wang X, Zhang K, Lacey M, Zhang H, Yin Q, Cameron J, Lin Z, Zhu D, Flemington EK. Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq. RNA. 2010 Aug;16(8):1610-22. PMID: 20584899.

Hedges DJ, Burges D, Powell E, Almonte C, Huang J, Young S, Boese B, Schmidt M, Pericak-Vance MA, Martin E, Zhang X, Harkins TT, Züchner S. Exome sequencing of a multigenerational human pedigree. PloS One. 2009 4(12). PMID: 20011588. First author

Witherspoon, DJ, Watkins WS, Zhang Y, Xing J, Tolpinrud WL, Hedges DJ, Batzer MA and Jorde LB. Alu repeats increase local recombination rates. BMC Genomics. 2009 Nov 16;10(1):530. PMID: 19917129.

Ma DQ, Salyakina D, Jaworski JM, Konidari I, Whitehead PL, Andersen AN, Hoffman JD, Slifer SH, Hedges DJ, Cukier HN, Grisworld AJ, McCauley JL, Beecham GW, Wright HH, Abramson RK, Martin ER, Hussman JP, Gilbert JR, Cuccaro ML, Haines JL, Pericak-Vance MA. A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. Ann Hum Genet. May; 73(Pt 3):263-73. PMID: 19456320.

Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL. Diverse cis factors controlling Alu retrotransposition: What causes Alu elements to die? Genome Res. 2009 Apr; 19(4):545-55. PMID: 19273617.

Cukier HN, Pericak-Vance MA, Gilbert JR, Hedges DJ. Sample Degradation Leads to False Positive Copy Number Variation Calls in Multiplex Real-Time PCR Assays. Analytical Biochemistry. 2009 Mar 15; 386(2):288-290. PMID: 19121619. Corresponding author

Bochukova EG, Roscioli T, Hedges DJ, Taylor IB, Johnson D, David DJ, Deininger PL, Wilkie AOM. Rare mutations of FGFR2 causing Apert syndrome: identification of the first deletion, and an Alu element insertion from a new subfamily. Human Mutations. 2009 Feb; 30(2):204-11. PMID: 18726952.

Gu W, Castoe TA, Hedges DJ, Batzer MA, Pollock DD. Identification of repeat structure in large genomes using repeat probability clouds. Analytical Biochemistry. 2008 Sep 1; 380(1):77-83. PMID: 18541131

Gasior SL, Preston G, Hedges DJ, Gilbert N, Moran JV, Deininger PL. Characterization of pre- insertion loci of de novo L1 insertions. 2007 Gene. April 1; 390(1-2):190-8. PMID:17067767

Lee J, Cordaux R, Han K, Wang J, Hedges DJ, Liang P, Batzer MA. Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons. Gene. 2007 April 1; 390(1-2):18- 27. PMID:1705519

Full Publications List

Last update: June 2020