Multiomic profiling identifies predictors of survival in African American patients with acute myeloid leukemia.

Stiff A, Fornerod M, Kain BN, Nicolet D, Kelly BJ, Miller KE, Mrózek K, Boateng I, Bollas A, Garfinkle EAR, Momoh O, Fasola FA, Olawumi HO, Mencia-Trinchant N, Kloppers JF, van Marle AC, Hu E, Wijeratne S, Wheeler G, Walker CJ, Buss J, Heyrosa A, Desai H, Laganson A, Hamp E, Abu-Shihab Y, Abaza H, Kronen P, Sen S, Johnstone ME, Quinn K, Wronowski B, Hertlein E, Miles LA, Mims AS, Oakes CC, Blachly JS, Larkin KT, Mundy-Bosse B, Carroll AJ, Powell BL, Kolitz JE, Stone RM, Duarte C, Abbott D, Amaya ML, Jordan CT, Uy GL, Stock W, Archer KJ, Paskett ED, Guzman ML, Levine RL, Menghrajani K, Chakravarty D, Berger MF, Bottomly D, McWeeney SK, Tyner JW, Byrd JC, Salomonis N, Grimes HL, Mardis ER, Eisfeld AK

Nat Genet

Cellular taxonomy of the preleukemic bone marrow niche of acute myeloid leukemia.

Goda C, Kulkarni R, Bustos Y, Li W, Rudich A, Balcioglu O, Chidester S, Urs AP, Karunasiri M, Al-Marrawi Y, Korn E, Kanna S, Garfinkle EAR, Shah N, Wooten A, Mundy-Bosse B, Sehgal L, Zhang B, Marcucci G, Mardis ER, Garzon R, Bowman RL, Viny AD, Miles LA, Miller KE, Dorrance AM

Leukemia

Circumventing resistance within the Ewing sarcoma microenvironment by combinatorial innate immunotherapy.

Luo W, Hoang H, Zhu H, Miller K, Mo X, Eguchi S, Tian M, Liao Y, Ayello J, Rosenblum JM, Marcondes M, Currier M, Mardis E, Cripe T, Lee D, Cairo MS

J Immunother Cancer

Combinatorial macrophage induced innate immunotherapy against Ewing sarcoma: Turning "Two Keys" simultaneously.

Luo W, Hoang H, Miller KE, Zhu H, Xu S, Mo X, Garfinkle EAR, Costello H, Wijeratne S, Chemnitz W, Gandhi R, Liao Y, Ayello J, Gardenswartz A, Rosenblum JM, Cassady KA, Mardis ER, Lee DA, Cripe TP, Cairo MS

J Exp Clin Cancer Res

Improvement of tumor neoantigen detection by high field asymmetric waveform ion mobility mass spectrometry.

Meng W, Takeuchi Y, Ward JP, Sultan H, Arthur CD, Mardis ER, Artyomov MN, Lichti CF, Schreiber RD

Cancer Immunol Res

A novel IKZF1 variant in a family with autosomal dominant CVID: A case for expanding exon coverage in inborn errors of immunity.

Stojkic I, Prince BT, Kuehn HS, Gil-Silva AA, Varga EA, Rosenzweig SD, Ramadesikan S, Supinger R, Marhabaie M, Chang P, Mardis ER, Koboldt DC

Clin Immunol

Integrating multisector molecular characterization into personalized peptide vaccine design for patients with newly diagnosed glioblastoma.

Johanns TM, Garfinkle EAR, Miller KE, Livingstone AJ, Roberts KF, Rao Venkata LP, Dowling JL, Chicoine MR, Dacey RG, Zipfel GJ, Kim AH, Mardis ER, Dunn GP

Clin Cancer Res

SNVstory: inferring genetic ancestry from genome sequencing data.

Bollas AE, Rajkovic A, Ceyhan D, Gaither JB, Mardis ER, White P

BMC Bioinformatics

Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity.

Wijeratne S, Gonzalez MEH, Roach K, Miller KE, Schieffer KM, Fitch JR, Leonard J, White P, Kelly BJ, Cottrell CE, Mardis ER, Wilson RK, Miller AR

BMC Genomics

Acute Myeloid Leukemia Genomics: Impact on Care and Remaining Challenges.

Eisfeld AK, Mardis ER

Clin Chem

A LINE-1 mediated deletion resulting in germline retinoblastoma predisposition.

Macke EL, Miller AR, Stonerock E, Olshefski R, Zajo K, Bedrosian TA, Mardis ER, Akkari YMN, Cottrell CE, Schieffer KM

Neurooncol Adv

Germline susceptibility from broad genomic profiling of pediatric brain cancers.

Mardis ER, Potter SL, Schieffer KM, Varga EA, Mathew MT, Costello HM, Wheeler G, Kelly BJ, Miller KE, Garfinkle EAR, Wilson RK, Cottrell CE

Neurooncol Adv

Corrigendum: Myelomodulatory treatments augment the therapeutic benefit of oncolytic viroimmunotherapy in murine models of malignant peripheral nerve sheath tumors.

Paudel SN, Hutzen BJ, Miller KE, Garfinkle EAR, Chen CY, Wang PY, Glaspell AM, Currier MA, Ringwalt EM, Boon L, Mardis ER, Cairo MS, Ratner N, Dodd RD, Cassady KA, Cripe TP

Front Immunol

Myelomodulatory treatments augment the therapeutic benefit of oncolytic viroimmunotherapy in murine models of malignant peripheral nerve sheath tumors.

Paudel SN, Hutzen BJ, Miller KE, Garfinkle EAR, Chen CY, Wang PY, Glaspell AM, Currier MA, Ringwalt EM, Boon L, Mardis ER, Cairo MS, Ratner N, Dodd RD, Cassady KA, Cripe TP

Front Immunol

Molecular characterization of gliomas and glioneuronal tumors amid Noonan syndrome: cancer predisposition examined.

Shatara M, Schieffer KM, Melas M, Varga EA, Thomas D, Bucknor BA, Costello HM, Wheeler G, Kelly BJ, Miller KE, Rodriguez DP, Mathew MT, Lee K, Crotty E, Leary S, Paulson VA, Cole B, Abdelbaki MS, Finlay JL, Lazow MA, Salloum R, Fouladi M, Boué DR, Mardis ER, Cottrell CE

Front Oncol

International symposium on inheritable central nervous system (CNS) cancer predisposition: A prologue.

Neurooncol Adv

Overview of modern genomic tools for diagnosis and precision therapy of childhood solid cancers.

Mardis ER

Curr Opin Pediatr

DGIdb 5.0: rebuilding the drug-gene interaction database for precision medicine and drug discovery platforms.

Cannon M, Stevenson J, Stahl K, Basu R, Coffman A, Kiwala S, McMichael JF, Kuzma K, Morrissey D, Cotto K, Mardis ER, Griffith OL, Griffith M, Wagner AH

Nucleic Acids Res

Childhood cancer data initiative: Status report.

Jagu S, Mardis ER, Wedekind MF, Widemann BC, Kingery RK, Gonzalez SL, Shern JF, Reaman GH

Pediatr Blood Cancer

Fatal brainstem injury following proton radiation in a patient with medulloblastoma and a germline variant in RNF213.

Klawinski DM, Cottrell CE, Schieffer KM, Indyk JA, Gandhi K, Mardis ER, Rodriguez DP, Breneman JC, Osorio DS

Pediatr Blood Cancer

Post-zygotic rescue of meiotic errors causes brain mosaicism and focal epilepsy.

Miller KE, Rivaldi AC, Shinagawa N, Sran S, Navarro JB, Westfall JJ, Miller AR, Roberts RD, Akkari Y, Supinger R, Hester ME, Marhabaie M, Gade M, Lu J, Rodziyevska O, Bhattacharjee MB, Von Allmen GK, Yang E, Lidov HGW, Harini C, Shah MN, Leonard J, Pindrik J, Shaikhouni A, Goldman JE, Pierson CR, Thomas DL, Boué DR, Ostendorf AP, Mardis ER, Poduri A, Koboldt DC, Heinzen EL, Bedrosian TA

Nat Genet

Novel inherited CDX2 variant segregating in a family with diverse congenital malformations of the genitourinary system.

Ramadesikan S, Colwell CM, Supinger R, Hunter J, Thomas J, Varga E, Mardis ER, Wood RJ, Koboldt DC

Cold Spring Harb Mol Case Stud

Oncolytic virus-driven immune remodeling revealed in mouse medulloblastomas at single cell resolution.

Hedberg J, Studebaker A, Smith L, Chen CY, Westfall JJ, Cam M, Gross A, Hernandez-Aguirre I, Martin A, Kim D, Dhital R, Kim Y, Roberts RD, Cripe TP, Mardis ER, Cassady KA, Leonard J, Miller KE

Mol Ther Oncolytics

10-Patient Trial: Remarkable Responses in Pediatric Cancers.

Mardis ER

Clin Cancer Res

Genetically modified IL2 bone-marrow-derived myeloid cells reprogram the glioma immunosuppressive tumor microenvironment.

Canella A, Nazzaro M, Rajendran S, Schmitt C, Haffey A, Nigita G, Thomas D, Lyberger JM, Behbehani GK, Amankulor NM, Mardis ER, Cripe TP, Rajappa P

Cell Rep

A chance encounter leads into immunogenomics.

Mardis ER

Nat Cancer

A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer.

Mayoh C, Gifford AJ, Terry R, Lau LMS, Wong M, Rao P, Shai-Hee T, Saletta F, Khuong-Quang DA, Qin V, Mateos MK, Meyran D, Miller KE, Yuksel A, Mould EVA, Bowen-James R, Govender D, Senapati A, Zhukova N, Omer N, Dholaria H, Alvaro F, Tapp H, Diamond Y, Pozza LD, Moore AS, Nicholls W, Gottardo NG, McCowage G, Hansford JR, Khaw SL, Wood PJ, Catchpoole D, Cottrell CE, Mardis ER, Marshall GM, Tyrrell V, Haber M, Ziegler DS, Vittorio O, Trapani JA, Cowley MJ, Neeson PJ, Ekert PG

Genome Med

Accurate diagnosis of pediatric brain cancers.

Bandopadhayay P, Mardis ER

Nat Med

Single-nuclei transcriptomics enable detection of somatic variants in patient brain tissue.

Townsend SE, Westfall JJ, Navarro JB, Koboldt DC, Mardis ER, Miller KE, Bedrosian TA

Sci Rep

Biallelic variants in HTRA2 cause 3-methylglutaconic aciduria mitochondrial disorder: case report and literature review.

Gurusamy U, Ramadesikan S, Marhabaie M, Colwell CM, Hunter JM, Leung ML, Mardis ER, White P, Manickam M, Wilson RK, Koboldt DC

Front Genet

Manufacture and Characterization of GMP-Compliant SARS-COV-2 Cytotoxic T Lymphocytes.

Chu Y, Milner J, Lamb M, Maryamchik E, Rigot O, Ayello J, Harrison L, Shaw R, Behbehani GK, Mardis ER, Miller K, Venkata LPR, Chang H, Lee D, Rosenthal E, Kadauke S, Bunin N, Talano JA, Johnson B, Wang Y, Cairo MS

J Infect Dis

Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis.

Garcia-Recio S, Hinoue T, Wheeler GL, Kelly BJ, Garrido-Castro AC, Pascual T, De Cubas AA, Xia Y, Felsheim BM, McClure MB, Rajkovic A, Karaesmen E, Smith MA, Fan C, Ericsson PIG, Sanders ME, Creighton CJ, Bowen J, Leraas K, Burns RT, Coppens S, Wheless A, Rezk S, Garrett AL, Parker JS, Foy KK, Shen H, Park BH, Krop I, Anders C, Gastier-Foster J, Rimawi MF, Nanda R, Lin NU, Isaacs C, Marcom PK, Storniolo AM, Couch FJ, Chandran U, Davis M, Silverstein J, Ropelewski A, Liu MC, Hilsenbeck SG, Norton L, Richardson AL, Symmans WF, Wolff AC, Davidson NE, Carey LA, Lee AV, Balko JM, Hoadley KA, Laird PW, Mardis ER, King TA, AURORA US Network , Perou CM

Nat Cancer

Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries.

Fernandez-Rozadilla C, Timofeeva M, Chen Z, Law P, Thomas M, Schmit S, Díez-Obrero V, Hsu L, Fernandez-Tajes J, Palles C, Sherwood K, Briggs S, Svinti V, Donnelly K, Farrington S, Blackmur J, Vaughan-Shaw P, Shu XO, Long J, Cai Q, Guo X, Lu Y, Broderick P, Studd J, Huyghe J, Harrison T, Conti D, Dampier C, Devall M, Schumacher F, Melas M, Rennert G, Obón-Santacana M, Martín-Sánchez V, Moratalla-Navarro F, Oh JH, Kim J, Jee SH, Jung KJ, Kweon SS, Shin MH, Shin A, Ahn YO, Kim DH, Oze I, Wen W, Matsuo K, Matsuda K, Tanikawa C, Ren Z, Gao YT, Jia WH, Hopper J, Jenkins M, Win AK, Pai R, Figueiredo J, Haile R, Gallinger S, Woods M, Newcomb P, Duggan D, Cheadle J, Kaplan R, Maughan T, Kerr R, Kerr D, Kirac I, Böhm J, Mecklin LP, Jousilahti P, Knekt P, Aaltonen L, Rissanen H, Pukkala E, Eriksson J, Cajuso T, Hänninen U, Kondelin J, Palin K, Tanskanen T, Renkonen-Sinisalo L, Zanke B, Männistö S, Albanes D, Weinstein S, Ruiz-Narvaez E, Palmer J, Buchanan D, Platz E, Visvanathan K, Ulrich C, Siegel E, Brezina S, Gsur A, Campbell P, Chang-Claude J, Hoffmeister M, Brenner H, Slattery M, Potter J, Tsilidis K, Schulze M, Gunter M, Murphy N, Castells A, Castellví-Bel S, Moreira L, Arndt V, Shcherbina A, Stern M, Pardamean B, Bishop T, Giles G, Southey M, Idos G, McDonnell K, Abu-Ful Z, Greenson J, Shulman K, Lejbkowicz F, Offit K, Su YR, Steinfelder R, Keku T, van Guelpen B, Hudson T, Hampel H, Pearlman R, Berndt S, Hayes R, Martinez ME, Thomas S, Corley D, Pharoah P, Larsson S, Yen Y, Lenz HJ, White E, Li L, Doheny K, Pugh E, Shelford T, Chan A, Cruz-Correa M, Lindblom A, Hunter D, Joshi A, Schafmayer C, Scacheri P, Kundaje A, Nickerson D, Schoen R, Hampe J, Stadler Z, Vodicka P, Vodickova L, Vymetalkova V, Papadopoulos N, Edlund C, Gauderman W, Thomas D, Shibata D, Toland A, Markowitz S, Kim A, Chanock S, van Duijnhoven F, Feskens E, Sakoda L, Gago-Dominguez M, Wolk A, Naccarati A, Pardini B, FitzGerald L, Lee SC, Ogino S, Bien S, Kooperberg C, Li C, Lin Y, Prentice R, Qu C, Bézieau S, Tangen C, Mardis E, Yamaji T, Sawada N, Iwasaki M, Haiman C, Le Marchand L, Wu A, Qu C, McNeil C, Coetzee G, Hayward C, Deary I, Harris S, Theodoratou E, Reid S, Walker M, Ooi LY, Moreno V, Casey G, Gruber S, Tomlinson I, Zheng W, Dunlop M, Houlston R, Peters U

Nat Genet

Myeloid cell heterogeneity in the tumor microenvironment and therapeutic implications for childhood central nervous system (CNS) tumors.

Kalathoor S, Rajendran S, Canella A, Raval R, Cripe TP, Mardis ER, Rajappa P

J Neuroimmunol

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.

Krysiak K, Danos AM, Saliba J, McMichael JF, Coffman AC, Kiwala S, Barnell EK, Sheta L, Grisdale CJ, Kujan L, Pema S, Lever J, Ridd S, Spies NC, Andric V, Chiorean A, Rieke DT, Clark KA, Reisle C, Venigalla AC, Evans M, Jani P, Takahashi H, Suda A, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Kesserwan C, Lamping M, Shen H, Marr AR, Hoang MH, Singhal K, Khanfar M, Li BV, Lin WH, Terraf P, Corson LB, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, King I, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith M, Griffith OL

Nucleic Acids Res

PacBio Fusion and Long Isoform Pipeline (PB_FLIP) for Cancer Transcriptome-based Resolution of Isoform Complexity.

Miller AR, Wijeratne S, McGrath SD, Schieffer KM, Miller KE, Lee K, Mathew M, LaHaye S, Fitch JR, Kelly BJ, White P, Mardis ER, Wilson RK, Cottrell CE, Magrini V

J Mol Diagn

Leveraging gene therapy to achieve long-term continuous or controllable expression of biotherapeutics.

Cripe TP, Hutzen B, Currier MA, Chen CY, Glaspell AM, Sullivan GC, Hurley JM, Deighen MR, Venkataramany AS, Mo X, Stanek JR, Miller AR, Wijeratne S, Magrini V, Mardis ER, Mendell JR, Chandler DS, Wang PY

Sci Adv

EGFR internal tandem duplications in fusion-negative congenital and neonatal spindle cell tumors.

Koo SC, Schieffer KM, Lee K, Gupta A, Pfau RB, Avenarius MR, Stonerock E, LaHaye S, Fitch J, Setty BA, Roberts R, Ranalli M, Conces MR, Bu F, Mardis ER, Cottrell CE

Genes Chromosomes Cancer

High early death rates, treatment resistance, and short survival of Black adolescents and young adults with AML.

Larkin K, Nicolet D, Kelly BJ, Mrózek K, LaHaye S, Miller KE, Wijeratne S, Wheeler GL, Kohlschmidt J, Blachly JS, Mims AS, Walker C, Oakes CC, Orwick S, Boateng I, Buss J, Heyrosa A, Desai H, Carroll AJ, Blum W, Powell BL, Kolitz JE, Moore JO, Mayer RJ, Larson RA, Stone RM, Paskett ED, Byrd JC, Mardis E, Eisfeld AK

Blood Adv

Infantile metastatic ependymoma with a novel molecular profile and favorable outcome to intensive chemotherapy without irradiation: case-based review.

Fw F, Schieffer KM, Cr P, Dr B, La Haye S, Miller KE, Amayiri N, Koboldt DC, Lichtenberg T, Leraas K, Brennan P, Kelly B, White P, Magrini V, Wilson RK, Mardis ER, Cottrell CE, Rusin J, Finlay JL, Osorio DS

Genes Chromosomes Cancer

Detection of brain somatic variation in epilepsy-associated developmental lesions.

Bedrosian TA, Miller KE, Grischow OE, Schieffer KM, LaHaye S, Yoon H, Miller AR, Navarro J, Westfall J, Leraas K, Choi S, Williamson R, Fitch J, Kelly BJ, White P, Lee K, McGrath S, Cottrell CE, Magrini V, Leonard J, Pindrik J, Shaikhouni A, Boué DR, Thomas DL, Pierson CR, Wilson RK, Ostendorf AP, Mardis ER, Koboldt DC

Epilepsia

Pediatric CNS cancer genomics and immunogenomics.

Miller KE, Mardis ER

Curr Opin Genet Dev

Acute lymphoblastic leukemia displays a distinct highly methylated genome.

Hetzel S, Mattei AL, Kretzmer H, Qu C, Chen X, Fan Y, Wu G, Roberts KG, Luger S, Litzow M, Rowe J, Paietta E, Stock W, Mardis ER, Wilson RK, Downing JR, Mullighan CG, Meissner A

Nat Cancer

A community approach to the cancer-variant-interpretation bottleneck.

Krysiak K, Danos AM, Kiwala S, McMichael JF, Coffman AC, Barnell EK, Sheta L, Saliba J, Grisdale CJ, Kujan L, Pema S, Lever J, Spies NC, Chiorean A, Rieke DT, Clark KA, Jani P, Takahashi H, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Lamping M, Marr AR, Li BV, Lin WH, Terraf P, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith OL, Griffith M

Nat Cancer

LINC00355 regulates p27KIP expression by binding to MENIN to induce proliferation in late-stage relapse breast cancer.

Eteleeb AM, Thunuguntla PK, Gelev KZ, Tang CY, Rozycki EB, Miller A, Lei JT, Jayasinghe RG, Dang HX, White NM, Reis-Filho JS, Mardis ER, Ellis MJ, Ding L, Silva-Fisher JM, Maher CA

NPJ Breast Cancer

Alternative RNA Splicing Defects in Pediatric Cancers: New Insights in Tumorigenesis and Potential Therapeutic Vulnerabilities.

Venkataramany AS, Schieffer KM, Lee K, Cottrell CE, Wang PY, Mardis ER, Cripe TP, Chandler DS

Ann Oncol

Expanding the Clinical Phenotype of FGFR1 Internal Tandem Duplication.

Kautto EA, Schieffer KM, McGrath S, Miller AR, Hernandez Gonzalez ME, Choi S, Conces MR, Fernandez-Faith E, Ho ML, Lee K, Lillis AP, Pearson GD, Kaler SG, Wilson RK, Mardis ER, Magrini V, Leonard J, Cottrell CE

Cold Spring Harb Mol Case Stud

Immune Activity and Response Differences of Oncolytic Viral Therapy in Recurrent Glioblastoma: Gene Expression Analyses of a Phase IB Study.

Miller KE, Cassady KA, Roth JC, Clements J, Schieffer KM, Leraas K, Miller AR, Prasad N, Leavenworth JW, Aban IB, Whitley RJ, Gillespie GY, Mardis ER, Markert JM

Clin Cancer Res

Clinical outcomes and efficacy of stereotactic body radiation therapy in children, Adolescents, and Young Adults with Metastatic Solid Tumors.

Baliga S, Matsui J, Klamer B, Cetnar A, Ewing A, Cadieux C, Gupta A, Setty BA, Roberts RD, Olshefski RS, Cripe TP, Scharschmidt TJ, Aldrink J, Mardis E, Yeager ND, Palmer JD

Br J Radiol

Molecular Heterogeneity in Pediatric Malignant Rhabdoid Tumors in Patients With Multi-Organ Involvement.

Miller KE, Wheeler G, LaHaye S, Schieffer KM, Cearlock S, Venkata LPR, Bravo AO, Grischow OE, Kelly BJ, White P, Pierson CR, Boué DR, Koo SC, Klawinski D, Ranalli MA, Shaikhouni A, Salloum R, Shatara M, Leonard JR, Wilson RK, Cottrell CE, Mardis ER, Koboldt DC

Front Oncol

Clinically aggressive pediatric spinal ependymoma with novel MYC amplification demonstrates molecular and histopathologic similarity to newly described MYCN-amplified spinal ependymomas.

Shatara M, Schieffer KM, Klawinski D, Thomas DL, Pierson CR, Sribnick EA, Jones J, Rodriguez DP, Deeg C, Hamelberg E, LaHaye S, Miller KE, Fitch J, Kelly B, Leraas K, Pfau R, White P, Magrini V, Wilson RK, Mardis ER, Abdelbaki MS, Finlay JL, Boué DR, Cottrell CE, Ghasemi DR, Pajtler KW, Osorio DS

Acta Neuropathol Commun

Discovery of clinically relevant fusions in pediatric cancer.

LaHaye S, Fitch JR, Voytovich KJ, Herman AC, Kelly BJ, Lammi GE, Arbesfeld JA, Wijeratne S, Franklin SJ, Schieffer KM, Bir N, McGrath SD, Miller AR, Wetzel A, Miller KE, Bedrosian TA, Leraas K, Varga EA, Lee K, Gupta A, Setty B, Boué DR, Leonard JR, Finlay JL, Abdelbaki MS, Osorio DS, Koo SC, Koboldt DC, Wagner AH, Eisfeld AK, Mrózek K, Magrini V, Cottrell CE, Mardis ER, Wilson RK, White P

BMC Genomics

The emergence of cancer genomics in diagnosis and precision medicine.

Mardis ER

Nat Cancer

Molecular and pathology features of colorectal tumors and patient outcomes are associated with Fusobacterium nucleatum and its subspecies animalis.

Borozan I, Zaidi SH, Harrison TA, Phipps AI, Zheng J, Lee S, Trinh QM, Steinfelder RS, Adams J, Banbury BL, Berndt SI, Brezina S, Buchanan DD, Bullman S, Cao Y, Farris AB, Figueiredo JC, Giannakis M, Heisler LE, Hopper JL, Lin Y, Luo X, Nishihara R, Mardis ER, Papadopoulos N, Qu C, Reid EEG, Thibodeau SN, Harlid S, Um CY, Hsu L, Gsur A, Campbell PT, Gallinger S, Newcomb PA, Ogino S, Sun W, Hudson TJ, Ferretti V, Peters U

Cancer Epidemiol Biomarkers Prev

Clinical Outcomes and Efficacy of Stereotactic Body Radiation Therapy in Metastatic Pediatric Solid Tumors.

Baliga S, Matsui JK, Klamer B, Cetnar A, Ewing A, Cadieux C, Gupta A, Setty B, Roberts R, Cripe TP, Scharschmidt T, Aldrink J, Mardis ER, Yeager ND, Olshefski R, Palmer JD

Int J Radiat Oncol Biol Phys

Somatic Variation as an Incidental Finding in the Pediatric Next Generation Sequencing Era.

Melas M, Mathew MT, Mori M, Jayaraman V, Wilson SA, Martin C, Jacobson-Kelly AE, Kelly BJ, Magrini V, Mardis ER, Cottrell CE, Lee K

Cold Spring Harb Mol Case Stud

Causal and Candidate Gene Variants in a Large Cohort of Women with Primary Ovarian Insufficiency.

Gorsi B, Hernandez E, Moore MB, Moriwaki M, Chow CY, Coelho E, Taylor E, Lu C, Walker A, Touraine P, Nelson LM, Cooper AR, Mardis ER, Rajkovic A, Yandell M, Welt CK

J Clin Endocrinol Metab

Targeted Therapy in a Young Adult With a Novel Epithelioid Tumor Driven by a PRRC2B-ALK Fusion.

Gupta A, Liu H, Schieffer KM, Koo SC, Cottrell CE, Mardis ER, Roberts RD, Yeager ND

J Natl Compr Canc Netw

Characterization of the Genomic and Immunological Diversity of Malignant Brain Tumors Through Multi-Sector Analysis.

Schaettler MO, Richters MM, Wang AZ, Skidmore ZL, Fisk B, Miller KE, Vickery TL, Kim AH, Chicoine MR, Osbun JW, Leuthardt EC, Dowling JL, Zipfel GJ, Dacey RG, Lu HC, Johanns TM, Griffith OL, Mardis ER, Griffith M, Dunn GP

Cancer Discov

Eliciting an immune-mediated antitumor response through oncolytic herpes simplex virus-based shared antigen expression in tumors resistant to viroimmunotherapy.

Ghonime MG, Saini U, Kelly MC, Roth JC, Wang PY, Chen CY, Miller K, Hernandez-Aguirre I, Kim Y, Mo X, Stanek JR, Cripe T, Mardis E, Cassady KA

J Immunother Cancer

Defining the AHR regulated transcriptome in NK cells reveal gene expression program relevant to development and function.

Trikha P, Moseman J, Thakkar A, Campbell AL, Elmas E, Foltz JA, Chakravarti N, Fitch J, Mardis E, Lee D

Blood Adv

Endogenous retrovirus envelope as a tumor-associated immunotherapeutic target in murine osteosarcoma.

Wedekind MF, Miller KE, Chen CY, Wang PY, Hutzen BJ, Currier MA, Nartker B, Roberts RD, Boon L, Conner J, LaHaye S, Kelly BJ, Gordon D, White P, Mardis ER, Cripe TP

iScience

PTEN somatic mutations contribute to spectrum of cerebral overgrowth.

Koboldt DC, Miller KE, Miller AR, Bush JM, McGrath S, Leraas K, Crist E, Fair S, Schwind W, Wijeratne S, Fitch J, Leonard J, Shaikhouni A, Hester ME, Magrini V, Ho ML, Pierson CR, Wilson RK, Ostendorf AP, Mardis ER, Bedrosian TA

Brain

Gastroblastoma with a Novel EWSR1-CTBP1 Fusion Presenting in Adolescence.

Koo SC, LaHaye S, Kovari BP, Schieffer KM, Ranalli MA, Aldrink JH, Michalsky MP, Colace S, Miller KE, Bedrosian TA, Leraas KM, Voytovich K, Wheeler G, Brennan P, Fitch J, Kelly BJ, McGrath SD, Miller AR, White P, Magrini V, Wilson RK, Mardis ER, Lauwers GY, Baker PB, Cottrell CE

Genes Chromosomes Cancer

Genomic prediction of neoantigens: immunogenomics before NGS.

Mardis ER

Nat Rev Genet

Novel Morphologic Findings in PLAG1-Rearranged Soft Tissue Tumors.

Logan SJ, Schieffer KM, Conces MR, Stonerock E, Miller AR, Fitch J, LaHaye S, Voytovich K, McGrath S, Magrini V, White P, Wilson RK, Mardis ER, Cottrell CE, Koo SC

Genes Chromosomes Cancer

Molecular classification of a complex structural rearrangement of the RB1 locus in an infant with sporadic, isolated, intracranial, sellar region retinoblastoma.

Schieffer KM, Feldman AZ, Kautto EA, McGrath S, Miller AR, Hernandez-Gonzalez ME, LaHaye S, Miller KE, Koboldt DC, Brennan P, Kelly B, Wetzel A, Agarwal V, Shatara M, Conley S, Rodriguez DP, Abu-Arja R, Shaikhkhalil A, Snuderl M, Orr BA, Finlay JL, Osorio DS, Drapeau AI, Leonard JR, Pierson CR, White P, Magrini V, Mardis ER, Wilson RK, Cottrell CE, Boué DR

Acta Neuropathol Commun

Clinical response to dabrafenib plus trametinib in a pediatric ganglioglioma with BRAF p.T599dup mutation.

Miller KE, Schieffer KM, Grischow O, Rodriguez DP, Cottrell CE, Leonard JR, Finlay JL, Mardis ER

Cold Spring Harb Mol Case Stud

Germline BAP1 Mutation in a Family With Multi-Generational Meningioma With Rhabdoid Features: A Case Series and Literature Review.

Prasad RN, Gardner UG, Yaney A, Prevedello DM, Koboldt DC, Thomas DL, Mardis ER, Palmer JD

Front Oncol

Association of 17q22 Amplicon Via Cell-Free DNA With Platinum Chemotherapy Response in Metastatic Triple-Negative Breast Cancer.

Collier KA, Asad S, Tallman D, Jenison J, Rajkovic A, Mardis ER, Parsons HA, Tolaney SM, Winer EP, Lin NU, Ha G, Adalsteinsson VA, Stover DG

JCO Precis Oncol

YAP1-FAM118B Fusion Defines a Rare Subset of Childhood and Young Adulthood Meningiomas.

Schieffer KM, Agarwal V, LaHaye S, Miller KE, Koboldt DC, Lichtenberg T, Leraas K, Brennan P, Kelly BJ, Crist E, Rusin J, Finlay JL, Osorio DS, Sribnick EA, Leonard JR, Feldman A, Orr BA, Serrano J, Vasudevaraja V, Snuderl M, White P, Magrini V, Wilson RK, Mardis ER, Boué DR, Cottrell CE

Am J Surg Pathol

Infantile fibrosarcoma-like tumor driven by novel RBPMS-MET fusion consolidated with cabozantinib.

Gupta A, Belsky JA, Schieffer KM, Leraas K, Varga E, McGrath SD, Koo SC, Magrini V, Wilson RK, White P, Mardis ER, Jatana KR, Cottrell CE, Setty BA

Cold Spring Harb Mol Case Stud

Somatic SLC35A2 mosaicism correlates with clinical findings in epilepsy brain tissue.

Miller KE, Koboldt DC, Schieffer KM, Bedrosian TA, Crist E, Sheline A, Leraas K, Magrini V, Zhong H, Brennan P, Bush J, Fitch J, Bir N, Miller AR, Cottrell CE, Leonard J, Pindrik JA, Rusin JA, Shah SH, White P, Wilson RK, Mardis ER, Pierson CR, Ostendorf AP

Neurol Genet

Genetic Characterization of Pediatric Sarcomas by Targeted RNA Sequencing.

Avenarius MR, Miller CR, Arnold MA, Koo S, Roberts R, Hobby M, Grossman T, Moyer Y, Wilson RK, Mardis ER, Gastier-Foster JM, Pfau R

J Mol Diagn

Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival.

Zaidi SH, Harrison TA, Phipps AI, Steinfelder R, Trinh QM, Qu C, Banbury BL, Georgeson P, Grasso CS, Giannakis M, Adams JB, Alwers E, Amitay EL, Barfield RT, Berndt SI, Borozan I, Brenner H, Brezina S, Buchanan DD, Cao Y, Chan AT, Chang-Claude J, Connolly CM, Drew DA, Farris AB, Figueiredo JC, French AJ, Fuchs CS, Garraway LA, Gruber S, Guinter MA, Hamilton SR, Harlid S, Heisler LE, Hidaka A, Hopper JL, Huang WY, Huyghe JR, Jenkins MA, Krzyzanowski PM, Lemire M, Lin Y, Luo X, Mardis ER, McPherson JD, Miller JK, Moreno V, Mu XJ, Nishihara R, Papadopoulos N, Pasternack D, Quist MJ, Rafikova A, Reid EEG, Shinbrot E, Shirts BH, Stein LD, Teney CD, Timms L, Um CY, Van Guelpen B, Van Tassel M, Wang X, Wheeler DA, Yung CK, Hsu L, Ogino S, Gsur A, Newcomb PA, Gallinger S, Hoffmeister M, Campbell PT, Thibodeau SN, Sun W, Hudson TJ, Peters U

Nat Commun

The clonal evolution of metastatic colorectal cancer.

Dang HX, Krasnick BA, White BS, Grossman JG, Strand MS, Zhang J, Cabanski CR, Miller CA, Fulton RS, Goedegebuure SP, Fronick CC, Griffith M, Larson DE, Goetz BD, Walker JR, Hawkins WG, Strasberg SM, Linehan DC, Lim KH, Lockhart AC, Mardis ER, Wilson RK, Ley TJ, Maher CA, Fields RC

Sci Adv

Disease-Associated Mosaic Variation in Clinical Exome Sequencing: A Two Year Pediatric Tertiary Care Experience.

Miller CR, Lee K, Pfau RB, Reshmi SC, Corsmeier DJ, Hashimoto S, Dave-Wala A, Jayaraman V, Koboldt DC, Matthews T, Mouhlas D, Stein M, McKinney A, Grossman T, Kelly BJ, White P, Magrini V, Wilson RK, Mardis ER, Cottrell CE

Cold Spring Harb Mol Case Stud

Long non-coding RNA RAMS11 promotes metastatic colorectal cancer progression.

Silva-Fisher JM, Dang HX, White NM, Strand MS, Krasnick BA, Rozycki EB, Jeffers GGL, Grossman JG, Highkin MK, Tang C, Cabanski CR, Eteleeb A, Mudd J, Goedegebuure SP, Luo J, Mardis ER, Wilson RK, Ley TJ, Lockhart AC, Fields RC, Maher CA

Nat Commun

Integrating Genetic and Genomic Testing Into Oncology Practice.

Domchek SM, Mardis E, Carlisle JW, Owonikoko TK

Am Soc Clin Oncol Educ Book