2024

A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma.

Weiner AK, Radaoui AB, Tsang M, Martinez D, Sidoli S, Conkrite KL, Delaidelli A, Modi A, Rokita JL, Patel K, Lane MV, Zhang B, Zhong C, Ennis B, Miller DP, Brown MA, Rathi KS, Raman P, Pogoriler J, Bhatti T, Pawel B, Glisovic-Aplenc T, Teicher B, Erickson SW, Earley EJ, Bosse KR, Sorensen PH, Krytska K, Mosse YP, Havenith KE, Zammarchi F, van Berkel PH, Smith MA, Garcia BA, Maris JM, Diskin SJ.bioRxiv. 2024 Jan 7:2023.12.06.570390. doi: 10.1101/2023.12.06.570390. Preprint.PMID: 38106022
[DOI]

BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma.

Randall MP, Egolf LE, Vaksman Z, Samanta M, Tsang M, Groff D, Evans JP, Rokita JL, Layeghifard M, Shlien A, Maris JM, Diskin SJ, Bosse KR.J Natl Cancer Inst. 2024 Jan 10;116(1):138-148. doi: 10.1093/jnci/djad182.PMID: 37688570
[DOI]

Germline pathogenic variants in neuroblastoma patients are enriched in BARD1 and predict worse survival.

Kim J, Vaksman Z, Egolf LE, Kaufman R, Evans JP, Conkrite KL, Danesh A, Lopez G, Randall MP, Dent MH, Farra LM, Menghani NL, Dymek M, Desai H, Hausler R, Hicks B, Auvil JG, Gerhard DS, Hakonarson H, Maxwell KN, Cole KA, Pugh TJ, Bosse KR, Khan J, Wei JS, Maris JM, Stewart DR, Diskin SJ.J Natl Cancer Inst. 2024 Jan 10;116(1):149-159. doi: 10.1093/jnci/djad183.PMID: 37688579
[DOI]

2023

Advancing childhood cancer research through young investigator and advocate collaboration.

Weiner AK, Palmer A, Moll MF, Lindberg G, Reidy K, Diskin SJ, Mackall CL, Maris JM, Sullivan PJ.bioRxiv. 2023 Dec 5:2023.12.03.569769. doi: 10.1101/2023.12.03.569769. Preprint.PMID: 38105944
[DOI]

Alternative lengthening of telomeres (ALT) in pediatric high-grade gliomas can occur without ATRX mutation and is enriched in patients with pathogenic germline mismatch repair (MMR) variants.

Stundon JL, Ijaz H, Gaonkar KS, Kaufman RS, Jin R, Karras A, Vaksman Z, Kim J, Corbett RJ, Lueder MR, Miller DP, Guo Y, Santi M, Li M, Lopez G, Storm PB, Resnick AC, Waanders AJ, MacFarland SP, Stewart DR, Diskin SJ, Rokita JL, Cole KA.Neuro Oncol. 2023 Jul 6;25(7):1331-1342. doi: 10.1093/neuonc/noac278.PMID: 36541551
[DOI]

AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.

Kim J, Naqvi AS, Corbett RJ, Kaufman RS, Vaksman Z, Brown MA, Miller DP, Phul S, Geng Z, Storm PB, Resnick AC, Stewart DR, Rokita JL, Diskin SJ.bioRxiv. 2023 Dec 1:2023.11.29.569103. doi: 10.1101/2023.11.29.569103. Preprint.PMID: 38076939
[DOI]

BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma.

Randall MP, Egolf LE, Vaksman Z, Samanta M, Tsang M, Groff D, Evans JP, Rokita JL, Layeghifard M, Shlien A, Maris JM, Diskin SJ, Bosse KR.bioRxiv. 2023 Feb 3:2023.01.31.525066. doi: 10.1101/2023.01.31.525066. Preprint.PMID: 36778420
[DOI]

Genetic Predisposition to Neuroblastoma Results from a Regulatory Polymorphism that Promotes the Adrenergic Cell State.

Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT.J Clin Invest. 2023 May 15;133(10):e166919. doi: 10.1172/JCI166919.PMID: 37183825
[DOI]

Germline pathogenic variants in 786 neuroblastoma patients.

Kim J, Vaksman Z, Egolf LE, Kaufman R, Evans JP, Conkrite KL, Danesh A, Lopez G, Randall MP, Dent MH, Farra LM, Menghani N, Dymek M, Desai H, Hausler R; Penn Medicine BioBank; Regeneron Genetics Center; Cancer Genomics Research Laboratory; Auvil JG, Gerhard DS, Hakonarson H, Maxwell KN, Cole KA, Pugh TJ, Bosse KR, Khan J, Wei JS, Maris JM, Stewart DR, Diskin SJ.medRxiv. 2023 Jan 25:2023.01.23.23284864. doi: 10.1101/2023.01.23.23284864. Preprint.PMID: 36747619
[DOI]

Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors.

Modi A, Lopez G, Conkrite KL, Su C, Leung TC, Ramanan S, Manduchi E, Johnson ME, Cheung D, Gadd S, Zhang J, Smith MA, Guidry Auvil JM, Meshinchi S, Perlman EJ, Hunger SP, Maris JM, Wells AD, Grant SFA, Diskin SJ.Cancer Res. 2023 Oct 13;83(20):3462-3477. doi: 10.1158/0008-5472.CAN-22-3186.PMID: 37584517
[DOI]

OpenPBTA: The Open Pediatric Brain Tumor Atlas.

Shapiro JA, Gaonkar KS, Spielman SJ, Savonen CL, Bethell CJ, Jin R, Rathi KS, Zhu Y, Egolf LE, Farrow BK, Miller DP, Yang Y, Koganti T, Noureen N, Koptyra MP, Duong N, Santi M, Kim J, Robins S, Storm PB, Mack SC, Lilly JV, Xie HM, Jain P, Raman P, Rood BR, Lulla RR, Nazarian J, Kraya AA, Vaksman Z, Heath AP, Kline C, Scolaro L, Viaene AN, Huang X, Way GP, Foltz SM, Zhang B, Poetsch AR, Mueller S, Ennis BM, Prados M, Diskin SJ, Zheng S, Guo Y, Kannan S, Waanders AJ, Margol AS, Kim MC, Hanson D, Van Kuren N, Wong J, Kaufman RS, Coleman N, Blackden C, Cole KA, Mason JL, Madsen PJ, Koschmann CJ, Stewart DR, Wafula E, Brown MA, Resnick AC, Greene CS, Rokita JL, Taroni JN; Children’s Brain Tumor Network; Pacific Pediatric Neuro-Oncology Consortium.Cell Genom. 2023 May 31;3(7):100340. doi: 10.1016/j.xgen.2023.100340. eCollection 2023 Jul 12.PMID: 37492101
[DOI]

Surface and global proteome analyses identify ENPP1 and other surface proteins as actionable immunotherapeutic targets in Ewing sarcoma.

Mooney B, Negri GL, Shyp T, Delaidelli A, Zhang HF, Spencer Miko SE, Weiner AK, Radaoui AB, Shraim R, Lizardo MM, Hughes CS, Li A, El-Naggar AM, Rouleau M, Li W, Dimitrov DS, Kurmasheva RT, Houghton PJ, Diskin SJ, Maris JM, Morin GB, Sorensen PH.Clin Cancer Res. 2023 Oct 9. doi: 10.1158/1078-0432.CCR-23-2187. Online ahead of print.PMID: 37812652
[DOI]

The Childhood Cancer Data Initiative: Using the Power of Data to Learn From and Improve Outcomes for Every Child and Young Adult With Pediatric Cancer.

Flores-Toro JA, Jagu S, Armstrong GT, Arons DF, Aune GJ, Chanock SJ, Hawkins DS, Heath A, Helman LJ, Janeway KA, Levine JE, Miller E, Penberthy L, Roberts CWM, Shalley ER, Shern JF, Smith MA, Staudt LM, Volchenboum SL, Zhang J, Zenklusen JC, Lowy DR, Sharpless NE, Guidry Auvil JM, Kerlavage AR, Widemann BC, Reaman GH, Kibbe WA, Doroshow JH; Childhood Cancer Data Initiative Working Groups.J Clin Oncol. 2023 Aug 20;41(24):4045-4053. doi: 10.1200/JCO.22.02208. Epub 2023 Jun 2.PMID: 37267580
[DOI]

2022

CFDP1 is a neuroblastoma susceptibility gene that regulates transcription factors of the noradrenergic cell identity.

Formicola D, Lasorsa VA, Cantalupo S, Testori A, Cardinale A, Avitabile M, Diskin S, Iolascon A, Capasso M.  CFDP1 is a neuroblastoma susceptibility gene that regulates transcription factors of the noradrenergic cell identity. HGG Adv. 2022 Nov 3;4(1):100158. doi: 10.1016/j.xhgg.2022.100158. PMID: 36425957; PMCID: PMC9678964.

[DOI]

Genetic Analysis in African American Children Supports Ancestry-Specific Neuroblastoma Susceptibility.

Testori A, Vaksman Z, Diskin SJ, Hakonarson H, Capasso M, Iolascon A, Maris JM, Devoto M.Cancer Epidemiol Biomarkers Prev. 2022 Apr 1;31(4):870-875. doi: 10.1158/1055-9965.EPI-21-0782.PMID: 35131881
[DOI]

Identification of Mitochondrial DNA Variants Associated With Risk of Neuroblastoma.

Chang X, Liu Y, Glessner J, Hou C, Qu H, Nguyen K, Sleiman P, Lee L, Diskin SJ, Maris JM, Hakonarson H.J Natl Cancer Inst. 2022 Jun 13;114(6):910-913. doi: 10.1093/jnci/djac012.PMID: 35134187
[DOI]

The children’s brain tumor network (CBTN) – Accelerating research in pediatric central nervous system tumors through collaboration and open science.

Lilly JV, Rokita JL, Mason JL, Patton T, Stefankiewiz S, Higgins D, Trooskin G, Larouci CA, Arya K, Appert E, Heath AP, Zhu Y, Brown MA, Zhang B, Farrow BK, Robins S, Morgan AM, Nguyen TQ, Frenkel E, Lehmann K, Drake E, Sullivan C, Plisiewicz A, Coleman N, Patterson L, Koptyra M, Helili Z, Van Kuren N, Young N, Kim MC, Friedman C, Lubneuski A, Blackden C, Williams M, Baubet V, Tauhid L, Galanaugh J, Boucher K, Ijaz H, Cole KA, Choudhari N, Santi M, Moulder RW, Waller J, Rife W, Diskin SJ, Mateos M, Parsons DW, Pollack IF, Goldman S, Leary S, Caporalini C, Buccoliero AM, Scagnet M, Haussler D, Hanson D, Firestein R, Cain J, Phillips JJ, Gupta N, Mueller S, Grant G, Monje-Deisseroth M, Partap S, Greenfield JP, Hashizume R, Smith A, Zhu S, Johnston JM, Fangusaro JR, Miller M, Wood MD, Gardner S, Carter CL, Prolo LM, Pisapia J, Pehlivan K, Franson A, Niazi T, Rubin J, Abdelbaki M, Ziegler DS, Lindsay HB, Stucklin AG, Gerber N, Vaske OM, Quinsey C, Rood BR, Nazarian J, Raabe E, Jackson EM, Stapleton S, Lober RM, Kram DE, Koschmann C, Storm PB, Lulla RR, Prados M, Resnick AC, Waanders AJ.Neoplasia. 2023 Jan;35:100846. doi: 10.1016/j.neo.2022.100846. Epub 2022 Nov 3.PMID: 36335802
[DOI]

2021

A G316A Polymorphism in the Ornithine Decarboxylase Gene Promoter Modulates MYCN-Driven Childhood Neuroblastoma.

Gamble LD, Purgato S, Henderson MJ, Di Giacomo S, Russell AJ, Pigini P, Murray J, Valli E, Milazzo G, Giorgi FM, Cowley M, Ashton LJ, Bhalshankar J, Schleiermacher G, Rihani A, Van Maerken T, Vandesompele J, Speleman F, Versteeg R, Koster J, Eggert A, Noguera R, Stallings RL, Tonini GP, Fong K, Vaksman Z, Diskin SJ, Maris JM, London WB, Marshall GM, Ziegler DS, Hogarty MD, Perini G, Norris MD, Haber M.Cancers (Basel). 2021 Apr 9;13(8):1807. doi: 10.3390/cancers13081807.PMID: 33918978
[DOI]

Correction to: Genetic susceptibility to neuroblastoma: current knowledge and future directions

Ritenour LE, Randall MP, Bosse KR, Diskin SJ. Correction to: Genetic susceptibility to neuroblastoma: current knowledge and future directions. Cell Tissue Res. 2021 Feb;383(2):905. doi: 10.1007/s00441-020-03277-8. Erratum for: Cell Tissue Res. 2018 May;372(2):287-307. PMID: 32897422

[DOI]

svpluscnv: analysis and visualization of complex structural variation data.

Lopez G, Egolf LE, Giorgi FM, Diskin SJ, Margolin AA.Bioinformatics. 2021 Jul 27;37(13):1912-1914. doi: 10.1093/bioinformatics/btaa878.PMID: 33051644
[DOI]

2020

European genetic ancestry associated with risk of childhood ependymoma

Zhang C, Ostrom QT, Hansen HM, Gonzalez-Maya J, Hu D, Ziv E, Morimoto L, de Smith AJ, Muskens IS, Kline CN, Vaksman Z, Hakonarson H, Diskin SJ, Kruchko C, Barnholtz-Sloan JS, Ramaswamy V, Ali-Osman F, Bondy ML, Taylor MD, Metayer C, Wiemels JL, Walsh KM. European genetic ancestry associated with risk of childhood ependymoma. Neuro Oncol. 2020 Nov 26;22(11):1637-1646. doi:
10.1093/neuonc/noaa130. PMID: 32607579; PMCID: PMC7846152.

Upton K, Modi A, Patel K, Kendsersky NM, Conkrite KL, Sussman RT, Way GP, Adams RN, Sacks GI, Fortina P, Diskin SJ, Maris JM, Rokita JL: Epigenomic profiling of neuroblastoma cell lines.

Sci Data. 2020 Apr 14;7(1):116. doi: 10.1038/s41597-020-0458-y.

[DOI]

Zhang C, Ostrom QT, Semmes EC, Ramaswamy V, Hansen HM, Morimoto L, de Smith
AJ, Pekmezci M, Vaksman Z, Hakonarson H, Diskin SJ, Metayer C; Glioma
International Case-Control Study (GICC); Taylor MD, Wiemels JL, Bondy ML, Walsh
KM. Genetic predisposition to longer telomere length and risk of childhood,
adolescent and adult-onset ependymoma. Acta Neuropathol Commun. 2020 Oct
28;8(1):173. doi: 10.1186/s40478-020-01038-w. PMID: 33115534; PMCID: PMC7592366

Chang X, Bakay M, Liu Y, Glessner J, Rathi KS, Hou C, Qu H, Vaksman Z, Nguyen K, Sleiman PMA, Diskin SJ, Maris JM, Hakonarson H: Mitochondrial DNA haplogroups and susceptibility to neuroblastoma.

J Natl Cancer Inst. 2020 Feb 25. pii: djaa024. doi: 10.1093/jnci/djaa024.

PMID:32096864
[DOI]

Mitochondrial DNA Haplogroups and Susceptibility to Neuroblastoma

Chang X, Bakay M, Liu Y, Glessner J, Rathi KS, Hou C, Qu H, Vaksman Z, Nguyen K, Sleiman PMA, Diskin SJ, Maris JM, Hakonarson H. Mitochondrial DNA Haplogroups and Susceptibility to Neuroblastoma. J Natl Cancer Inst. 2020 Dec 14;112(12):1259-1266. doi:10.1093/jnci/djaa024. PMID: 32096864; PMCID: PMC7735767.

[DOI]

Lopez G, Conkrite KL, Doepner M, Rathi KS, Modi A, Vaksman Z, Farra LM,
Hyson E, Noureddine M, Wei JS, Smith MA, Asgharzadeh S, Seeger RC, Khan J, Auvil
JG, Gerhard DS, Maris JM, Diskin SJ. Somatic structural variation targets
neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in
neuroblastoma. Genome Res. 2020 Sep;30(9):1228-1242. doi: 10.1101/gr.252106.119.
Epub 2020 Aug 13. PMID: 32796005; PMCID: PMC7545140.

[DOI]

Koneru B, Lopez G, Farooqi A, Conkrite KL, Nguyen TH, Macha SJ, Modi A, Rokita JL, Urias E, Hindle A, Davidson H, Mccoy K, Nance J, Yazdani V, Irwin MS, Yang S, Wheeler DA, Maris JM, Diskin SJ, Reynolds CP: Telomere maintenance mechanisms define clinical outcome in high-risk neuroblastoma.

Cancer Res. 2020 Apr 14. pii: canres.3068.2019. doi: 10.1158/0008-5472.CAN-19-3068.

[DOI]

Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe’er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH. Human Tumor Atlas Network. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.

Cell. 2020 Apr 16;181(2):236-249. doi: 10.1016/j.cell.2020.03.053. Review.

[DOI]

Ijaz H, Koptyra M, Gaonkar KS, Rokita JL, Baubet VP, Tauhid L, Zhu Y, Brown M, Lopez G, Zhang B, Diskin SJ, Vaksman Z, Children’s Brain Tumor Tissue Consortium, Mason JL, Appert E, Lilly J, Lulla R, De Raedt T, Heath AP, Felmeister A, Raman P, Nazarian J, Santi MR, Storm PB, Resnick A, Waanders AJ, Cole KA: Pediatric High Grade Glioma Resources From the Children’s Brain Tumor Tissue Consortium (CBTTC) and Pediatric Brain Tumor Atlas (PBTA).

Neuro Oncol. 2020 Jan 11;22(1):163-165. doi: 10.1093/neuonc/noz192.

[DOI]