CRISPR-Cas9 homology-independent targeted integration of exons 1–19 restores full-length dystrophin in mice

Authors: Stephenson, Anthony A., Nicolau, Stefan, Vetter, Tatyana A., Dufresne, Gabrielle P., Frair, Emma C., Sarff, Jessica E., Wheeler, Gregory L., Kelly, Benjamin J., White, Peter, Flanigan, Kevin M.

Source: In Molecular Therapy - Methods & Clinical Development 14 September 2023 30:486-499

Pacific Biosciences Fusion and Long Isoform Pipeline for Cancer Transcriptome–Based Resolution of Isoform Complexity

Authors: Miller, Anthony R., Wijeratne, Saranga, McGrath, Sean D., Schieffer, Kathleen M., Miller, Katherine E., Lee, Kristy, Mathew, Mariam, LaHaye, Stephanie, Fitch, James R., Kelly, Benjamin J., White, Peter, Mardis, Elaine R., Wilson, Richard K., Cottrell, Catherine E., Magrini, Vincent

Source: In The Journal of Molecular Diagnostics December 2022 24(12):1292-1306

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

Authors: Larkin, Karilyn T., Nicolet, Deedra, Kelly, Benjamin J., Mrózek, Krzysztof, LaHaye, Stephanie, Miller, Katherine E., Wijeratne, Saranga, Wheeler, Gregory, Kohlschmidt, Jessica, Blachly, James S., Mims, Alice S., Walker, Christopher J., Oakes, Christopher C., Orwick, Shelley, Boateng, Isaiah, Buss, Jill, Heyrosa, Adrienne, Desai, Helee, Carroll, Andrew J., Blum, William, Powell, Bayard L., Kolitz, Jonathan E., Moore, Joseph O., Mayer, Robert J., Larson, Richard A., Stone, Richard M., Paskett, Electra D., Byrd, John C., Mardis, Elaine R., Eisfeld, Ann-Kathrin

Source: In Blood Advances 11 October 2022 6(19):5570-5581

Detection of brain somatic variation in epilepsy‐associated developmental lesions

Authors: Bedrosian, Tracy A., Miller, Katherine E., Grischow, Olivia E., Schieffer, Kathleen M., LaHaye, Stephanie, Yoon, Hyojung, Miller, Anthony R., Navarro, Jason, Westfall, Jesse, Leraas, Kristen, Choi, Samantha, Williamson, Rachel, Fitch, James, Kelly, Benjamin J., White, Peter, Lee, Kristy, McGrath, Sean, Cottrell, Catherine E., Magrini, Vincent, Leonard, Jeffrey, Pindrik, Jonathan, Shaikhouni, Ammar, Boué, Daniel R., Thomas, Diana L., Pierson, Christopher R., Wilson, Richard K., Ostendorf, Adam P., Mardis, Elaine R., Koboldt, Daniel C.

Source: Epilepsia. 63(8):1981-1997

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100175701094.0x000001&indx=1&recIds=ETOCvdc_100175701094.0x000001

Evidence of pioneer factor activity of an oncogenic fusion transcription factor

Authors: Sunkel, Benjamin D., Wang, Meng, LaHaye, Stephanie, Kelly, Benjamin J., Fitch, James R., Barr, Frederic G., White, Peter, Stanton, Benjamin Z.

Source: In iScience 20 August 2021 24(8)

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

Authors: Wedekind, Mary Frances, Miller, Katherine E., Chen, Chun-Yu, Wang, Pin-Yi, Hutzen, Brian J., Currier, Mark A., Nartker, Brooke, Roberts, Ryan D., Boon, Louis, Conner, Joe, LaHaye, Stephanie, Kelly, Benjamin J., Gordon, David, White, Peter, Mardis, Elaine R., Cripe, Timothy P.

Source: In iScience 23 July 2021 24(7)

Gastroblastoma with a novel EWSR1‐CTBP1 fusion presenting in adolescence

Authors: Koo, Selene C., LaHaye, Stephanie, Kovari, Bence P., Schieffer, Kathleen M., Ranalli, Mark A., Aldrink, Jennifer H., Michalsky, Marc P., Colace, Susan, Miller, Katherine E., Bedrosian, Tracy A., Leraas, Kristen M., Voytovich, Kyle, Wheeler, Gregory, Brennan, Patrick, Fitch, James, Kelly, Benjamin J., McGrath, Sean D., Miller, Anthony R., White, Peter, Magrini, Vincent, Wilson, Richard K., Mardis, Elaine R., Lauwers, Gregory Y., Baker, Peter B., Cottrell, Catherine E.

Source: Genes, chromosomes & cancer. 60(9):640-646

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100137349154.0x000001&indx=1&recIds=ETOCvdc_100137349154.0x000001

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

Authors: Schieffer, Kathleen M., Agarwal, Vibhuti, LaHaye, Stephanie, Miller, Katherine E., Koboldt, Daniel C., Lichtenberg, Tara, Leraas, Kristen, Brennan, Patrick, Kelly, Benjamin J., Crist, Erin, Rusin, Jerome, Finlay, Jonathan L., Osorio, Diana S., Sribnick, Eric A., Leonard, Jeffrey R., Feldman, Alexander, Orr, Brent A., Serrano, Jonathan, Vasudevaraja, Varshini, Snuderl, Matija, White, Peter, Magrini, Vincent, Wilson, Richard K., Mardis, Elaine R., Boué, Daniel R., Cottrell, Catherine E.

Source: American journal of surgical pathology. 45(3):329-340

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185884893.0x000001&indx=1&recIds=ETOCvdc_100185884893.0x000001

Comprehensive genomic characterization of hematologic malignancies at a pediatric tertiary care center.

Authors: Kebede, Ann M., Garfinkle, Elizabeth A. R., Mathew, Mariam T., Varga, Elizabeth, Colace, Susan I., Wheeler, Gregory, Kelly, Benjamin J., Schieffer, Kathleen M., Miller, Katherine E., Mardis, Elaine R., Cottrell, Catherine E., Potter, Samara L.

Source: Frontiers in Oncology; 2024, p1-12, 12p

Subject Terms: NUCLEOTIDE sequencing, SINGLE nucleotide polymorphisms, HEMATOLOGIC malignancies, PEDIATRIC oncology, PEDIATRIC therapy

Correspondence comprehensive characterization of a brainstem aggregoma (light and heavy chain deposition disease)

Authors: Becker, Aline P., Osorio, Diana S., Bell, Erica H., Giglio, Pierre, Fleming, Jessica L., Cottrell, Catherine E., Mardis, Elaine R., Miller, Katherine E., Schieffer, Kathleen M., Kelly, Benjamin J., Makary, Mina S., Slone, Wayne, Benson, Don, Leonard, Jeffrey, Kahwash, Samir B., Boué, Daniel R., Chakravarti, Arnab

Source: Brain pathology. 33(5)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100191750219.0x000001&indx=1&recIds=ETOCvdc_100191750219.0x000001

Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads

Authors: Darby, Charlotte A., Fitch, James R., Brennan, Patrick J., Kelly, Benjamin J., Bir, Natalie, Magrini, Vincent, Leonard, Jeffrey, Cottrell, Catherine E., Gastier-Foster, Julie M., Wilson, Richard K., Mardis, Elaine R., White, Peter, Langmead, Ben, Schatz, Michael C.

Source: In iScience 30 August 2019 18:1-10

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

Authors: Stiff, Andrew, Fornerod, Maarten, Kain, Bailee N., Nicolet, Deedra, Kelly, Benjamin J., Miller, Katherine E., Mrózek, Krzysztof, Boateng, Isaiah, Bollas, Audrey, Garfinkle, Elizabeth A. R., Momoh, Omolegho, Fasola, Foluke A., Olawumi, Hannah O., Mencia-Trinchant, Nuria, Kloppers, Jean F., van Marle, Anne-Cecilia, Hu, Eileen, Wijeratne, Saranga, Wheeler, Gregory, Walker, Christopher J., Buss, Jill, Heyrosa, Adrienne, Desai, Helee, Laganson, Andrea, Hamp, Ethan, Abu-Shihab, Yazan, Abaza, Hasan, Kronen, Parker, Sen, Sidharth, Johnstone, Megan E., Quinn, Kate, Wronowski, Ben, Hertlein, Erin, Miles, Linde A., Mims, Alice S., Oakes, Christopher C., Blachly, James S., Larkin, Karilyn T., Mundy-Bosse, Bethany, Carroll, Andrew J., Powell, Bayard L., Kolitz, Jonathan E., Stone, Richard M., Duarte, Cassandra, Abbott, Diana, Amaya, Maria L., Jordan, Craig T., Uy, Geoffrey L., Stock, Wendy, Archer, Kellie J., Paskett, Electra D., Guzman, Monica L., Levine, Ross L., Menghrajani, Kamal, Chakravarty, Debyani, Berger, Michael F., Bottomly, Daniel, McWeeney, Shannon K., Tyner, Jeffrey W., Byrd, John C., Salomonis, Nathan, Grimes, H. Leighton, Mardis, Elaine R., Eisfeld, Ann-Kathrin

Source: Nature Genetics; November 2024, Vol. 56 Issue: 11 p2434-2446, 13p

A Proposed Statistical Protocol for the Analysis of Metabolic Toxicological Data Derived from NMR Spectroscopy

Authors: Kelly, Benjamin J., Anderson, Paul E., Reo, Nicholas V., DelRaso, Nicholas J., Doom, Travis E., Raymer, Michael L.

Source: 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on. :1414-1418 Oct, 2007

Relation: 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering

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

Authors: Shatara, Margaret, Schieffer, Kathleen M., Melas, Marilena, Varga, Elizabeth A., Thomas, Diana, Bucknor, Brianna A., Costello, Heather M., Wheeler, Gregory, Kelly, Benjamin J., Miller, Katherine E., Rodriguez, Diana P., Mathew, Mariam T., Lee, Kristy, Crotty, Erin, Leary, Sarah, Paulson, Vera A., Cole, Bonnie, Abdelbaki, Mohamed S., Finlay, Jonathan L., Lazow, Margot A.

Source: Frontiers in Oncology; 2024, p1-17, 17p

Subject Terms: NOONAN syndrome, TUMOR classification, YOUNG adults, DNA analysis, NUCLEOTIDE sequencing

Salivary gland carcinosarcoma ex pleomorphic adenoma: a case report with molecular characterization.

Authors: Javaid, Sehrish, Wang, Daren, Kelly, Benjamin J, Kalim, Sonya, Yanich, Jason, Kalmar, John R., Mallery, Susan R.

Source: Oral Surgery, Oral Medicine, Oral Pathology & Oral Radiology; Aug2024, Vol. 138 Issue 2, p301-305, 5p

Increase in Full-Length Dystrophin by Exon Skipping in Duchenne Muscular Dystrophy Patients with Single Exon Duplications: An Open-label Study.

Authors: Nicolau, Stefan, Malhotra, Jyoti, Kaler, Maryann, Magistrado-Coxen, Pamela, Iammarino, Megan A., Reash, Natalie F., Frair, Emma C., Wijeratne, Saranga, Kelly, Benjamin J., White, Peter, Lowes, Linda P., Waldrop, Megan A., Flanigan, Kevin M.

Source: Journal of Neuromuscular Diseases; 2024, Vol. 11 Issue 3, p679-685, 7p

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

Authors: Wijeratne, Saranga, Gonzalez, Maria E. Hernandez, Roach, Kelli, Miller, Katherine E., Schieffer, Kathleen M., Fitch, James R., Leonard, Jeffrey, White, Peter, Kelly, Benjamin J., Cottrell, Catherine E., Mardis, Elaine R., Wilson, Richard K., Miller, Anthony R.

Source: BMC Genomics; 1/29/2024, Vol. 25 Issue 1, p1-19, 19p

Germline susceptibility from broad genomic profiling of pediatric brain cancers.

Authors: Mardis, Elaine R, Potter, Samara L, Schieffer, Kathleen M, Varga, Elizabeth A, Mathew, Mariam T, Costello, Heather M, Wheeler, Gregory, Kelly, Benjamin J, Miller, Katherine E, Garfinkle, Elizabeth A R, Wilson, Richard K, Cottrell, Catherine E

Source: Neuro-Oncology Advances; Jan-Dec2024, Vol. 6 Issue 1, p1-10, 10p

Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population

Authors: Gaither, Jeffrey B S, Lammi, Grant E, Li, James L, Gordon, David M, Kuck, Harkness C, Kelly, Benjamin J, Fitch, James R, White, Peter

Source: GigaScience. 10(4)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100119662967.0x000001&indx=1&recIds=ETOCvdc_100119662967.0x000001

Exome sequencing in multiplex families with left-sided cardiac defects has high yield for disease gene discovery.

Authors: Gordon, David M.¹, Cunningham, David², Zender, Gloria², Lawrence, Patrick J.^1,2, Penaloza, Jacqueline S.¹, Lin, Hui², Fitzgerald-Butt, Sara M.^2,3, Myers, Katherine², Duong, Tiffany², Corsmeier, Donald J.¹, Gaither, Jeffrey B.¹, Kuck, Harkness C.¹, Wijeratne, Saranga¹, Moreland, Blythe¹, Kelly, Benjamin J.¹, Garg, Vidu^2,3, White, Peter^1,3, McBride, Kim L.^2,3, kim.mcbride@nationwidechildrens.org

Source: PLoS Genetics; 6/23/2022, Vol. 18 Issue 6, p1-25, 25p