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Items: 25

1.

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.

Song N, Li Z, Qin N, Howell CR, Wilson CL, Easton J, Mulder HL, Edmonson MN, Rusch M, Zhang J, Hudson MM, Yasui Y, Robison LL, Ness KK, Wang Z.

Clin Cancer Res. 2020 Jan 22. pii: clincanres.2503.2019. doi: 10.1158/1078-0432.CCR-19-2503. [Epub ahead of print]

PMID:
31969337
2.

Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia.

Li B, Brady SW, Ma X, Shen S, Zhang Y, Li Y, Szlachta K, Dong L, Liu Y, Yang F, Wang N, Flasch DA, Myers MA, Mulder HL, Ding L, Liu Y, Tian L, Hagiwara K, Xu K, Zhou X, Sioson E, Wang T, Yang L, Zhao J, Zhang H, Shao Y, Sun H, Sun L, Cai J, Sun HY, Lin TN, Du L, Li H, Rusch M, Edmonson MN, Easton J, Zhu X, Zhang J, Cheng C, Raphael BJ, Tang J, Downing JR, Alexandrov LB, Zhou BS, Pui CH, Yang JJ, Zhang J.

Blood. 2020 Jan 2;135(1):41-55. doi: 10.1182/blood.2019002220.

PMID:
31697823
3.

Molecular Mechanism of Telomere Length Dynamics and Its Prognostic Value in Pediatric Cancers.

Wang Z, Rice SV, Chang TC, Liu Y, Liu Q, Qin N, Putnam DK, Shelton K, Lanctot JQ, Wilson CL, Ness KK, Rusch MC, Edmonson MN, Wu G, Easton J, Kesserwan CA, Downing JR, Chen X, Nichols KE, Yasui Y, Robison LL, Zhang J.

J Natl Cancer Inst. 2019 Oct 24. pii: djz210. doi: 10.1093/jnci/djz210. [Epub ahead of print]

PMID:
31647544
4.

Enrichment of heterozygous germline RECQL4 loss-of-function variants in pediatric osteosarcoma.

Maciaszek JL, Oak N, Chen W, Hamilton KV, McGee RB, Nuccio R, Mostafavi R, Hines-Dowell S, Harrison L, Taylor L, Gerhardt EL, Ouma A, Edmonson MN, Patel A, Nakitandwe J, Pappo AS, Azzato EM, Shurtleff SA, Ellison DW, Downing JR, Hudson MM, Robison LL, Santana V, Newman S, Zhang J, Wang Z, Wu G, Nichols KE, Kesserwan CA.

Cold Spring Harb Mol Case Stud. 2019 Oct 23;5(5). pii: a004218. doi: 10.1101/mcs.a004218. Print 2019 Oct.

5.

RNAIndel: discovering somatic coding indels from tumor RNA-Seq data.

Hagiwara K, Ding L, Edmonson MN, Rice SV, Newman S, Easton J, Dai J, Meshinchi S, Ries RE, Rusch M, Zhang J.

Bioinformatics. 2019 Oct 8. pii: btz753. doi: 10.1093/bioinformatics/btz753. [Epub ahead of print]

PMID:
31593214
6.

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

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.

Genome Res. 2019 Sep;29(9):1555-1565. doi: 10.1101/gr.250357.119. Epub 2019 Aug 22.

7.

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

Ma X, Shao Y, Tian L, Flasch DA, Mulder HL, Edmonson MN, Liu Y, Chen X, Newman S, Nakitandwe J, Li Y, Li B, Shen S, Wang Z, Shurtleff S, Robison LL, Levy S, Easton J, Zhang J.

Genome Biol. 2019 Mar 14;20(1):50. doi: 10.1186/s13059-019-1659-6.

8.

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

Brady SW, Ma X, Bahrami A, Satas G, Wu G, Newman S, Rusch M, Putnam DK, Mulder HL, Yergeau DA, Edmonson MN, Easton J, Alexandrov LB, Chen X, Mardis ER, Wilson RK, Downing JR, Pappo AS, Raphael BJ, Dyer MA, Zhang J.

Mol Cancer Res. 2019 Apr;17(4):895-906. doi: 10.1158/1541-7786.MCR-18-0620. Epub 2019 Jan 16.

PMID:
30651371
9.

Corrigendum: Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping.

Wu G, Fan L, Edmonson MN, Shaw T, Boggs K, Easton J, Rusch MC, Webb TR, Zhang J, Potter PM.

RNA. 2018 Dec;24(12):1886. doi: 10.1261/rna.068544.118. No abstract available.

10.

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

Wang Z, Liu Q, Wilson CL, Easton J, Mulder H, Chang TC, Rusch MC, Edmonson MN, Rice SV, Ehrhardt MJ, Howell RM, Kesserwan CA, Wu G, Nichols KE, Downing JR, Hudson MM, Zhang J, Yasui Y, Robison LL.

Clin Cancer Res. 2018 Dec 15;24(24):6230-6235. doi: 10.1158/1078-0432.CCR-18-1775. Epub 2018 Oct 26.

11.

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

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.

Nat Commun. 2018 Sep 27;9(1):3962. doi: 10.1038/s41467-018-06485-7.

12.

Genetic Risk for Subsequent Neoplasms Among Long-Term Survivors of Childhood Cancer.

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.

J Clin Oncol. 2018 Jul 10;36(20):2078-2087. doi: 10.1200/JCO.2018.77.8589. Epub 2018 May 30.

13.

Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping.

Wu G, Fan L, Edmonson MN, Shaw T, Boggs K, Easton J, Rusch MC, Webb TR, Zhang J, Potter PM.

RNA. 2018 Aug;24(8):1056-1066. doi: 10.1261/rna.065383.117. Epub 2018 May 29. Erratum in: RNA. 2018 Dec;24(12):1886.

14.

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours.

Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, Zhou X, Li Y, Rusch MC, Easton J, Huether R, Gonzalez-Pena V, Wilkinson MR, Hermida LC, Davis S, Sioson E, Pounds S, Cao X, Ries RE, Wang Z, Chen X, Dong L, Diskin SJ, Smith MA, Guidry Auvil JM, Meltzer PS, Lau CC, Perlman EJ, Maris JM, Meshinchi S, Hunger SP, Gerhard DS, Zhang J.

Nature. 2018 Mar 15;555(7696):371-376. doi: 10.1038/nature25795. Epub 2018 Feb 28.

15.

The neoepitope landscape in pediatric cancers.

Chang TC, Carter RA, Li Y, Li Y, Wang H, Edmonson MN, Chen X, Arnold P, Geiger TL, Wu G, Peng J, Dyer M, Downing JR, Green DR, Thomas PG, Zhang J.

Genome Med. 2017 Aug 31;9(1):78. doi: 10.1186/s13073-017-0468-3.

16.

Exploring genomic alteration in pediatric cancer using ProteinPaint.

Zhou X, Edmonson MN, Wilkinson MR, Patel A, Wu G, Liu Y, Li Y, Zhang Z, Rusch MC, Parker M, Becksfort J, Downing JR, Zhang J.

Nat Genet. 2016 Jan;48(1):4-6. doi: 10.1038/ng.3466. No abstract available.

17.

Germline Mutations in Predisposition Genes in Pediatric Cancer.

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.

N Engl J Med. 2015 Dec 10;373(24):2336-2346. doi: 10.1056/NEJMoa1508054. Epub 2015 Nov 18.

18.

The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes.

Huether R, Dong L, Chen X, Wu G, Parker M, Wei L, Ma J, Edmonson MN, Hedlund EK, Rusch MC, Shurtleff SA, Mulder HL, Boggs K, Vadordaria B, Cheng J, Yergeau D, Song G, Becksfort J, Lemmon G, Weber C, Cai Z, Dang J, Walsh M, Gedman AL, Faber Z, Easton J, Gruber T, Kriwacki RW, Partridge JF, Ding L, Wilson RK, Mardis ER, Mullighan CG, Gilbertson RJ, Baker SJ, Zambetti G, Ellison DW, Zhang J, Downing JR.

Nat Commun. 2014 Apr 8;5:3630. doi: 10.1038/ncomms4630.

19.

Genome-wide transcriptional sequencing identifies novel mutations in metabolic genes in human hepatocellular carcinoma.

Meerzaman DM, Yan C, Chen QR, Edmonson MN, Schaefer CF, Clifford RJ, Dunn BK, Dong L, Finney RP, Cultraro CM, Hu Y, Yang Z, Nguyen CV, Kelley JM, Cai S, Zhang H, Zhang J, Wilson R, Messmer L, Chung YH, Kim JA, Park NH, Lyu MS, Song IH, Komatsoulis G, Buetow KH.

Cancer Genomics Proteomics. 2014 Jan-Feb;11(1):1-12.

PMID:
24633315
20.

Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia.

Roberts KG, Morin RD, Zhang J, Hirst M, Zhao Y, Su X, Chen SC, Payne-Turner D, Churchman ML, Harvey RC, Chen X, Kasap C, Yan C, Becksfort J, Finney RP, Teachey DT, Maude SL, Tse K, Moore R, Jones S, Mungall K, Birol I, Edmonson MN, Hu Y, Buetow KE, Chen IM, Carroll WL, Wei L, Ma J, Kleppe M, Levine RL, Garcia-Manero G, Larsen E, Shah NP, Devidas M, Reaman G, Smith M, Paugh SW, Evans WE, Grupp SA, Jeha S, Pui CH, Gerhard DS, Downing JR, Willman CL, Loh M, Hunger SP, Marra MA, Mullighan CG.

Cancer Cell. 2012 Aug 14;22(2):153-66. doi: 10.1016/j.ccr.2012.06.005.

21.

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.

Edmonson MN, Zhang J, Yan C, Finney RP, Meerzaman DM, Buetow KH.

Bioinformatics. 2011 Mar 15;27(6):865-6. doi: 10.1093/bioinformatics/btr032. Epub 2011 Jan 28.

22.

Bioinformatics tools for single nucleotide polymorphism discovery and analysis.

Clifford RJ, Edmonson MN, Nguyen C, Scherpbier T, Hu Y, Buetow KH.

Ann N Y Acad Sci. 2004 May;1020:101-9. Review.

PMID:
15208187
23.

Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms.

Clifford RJ, Edmonson MN, Nguyen C, Buetow KH.

Bioinformatics. 2004 May 1;20(7):1006-14. Epub 2004 Jan 29.

PMID:
14751981
24.

A phylogenetic analysis identifies heterogeneity among hepatocellular carcinomas.

McGlynn KA, Edmonson MN, Michielli RA, London WT, Lin WY, Chen GC, Shen FM, Buetow KH.

Hepatology. 2002 Dec;36(6):1341-8.

PMID:
12447857
25.

Reliable identification of large numbers of candidate SNPs from public EST data.

Buetow KH, Edmonson MN, Cassidy AB.

Nat Genet. 1999 Mar;21(3):323-5.

PMID:
10080189

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