Category: 2023

Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup U

Walker LC, Hoya M, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB; ClinGen Sequence Variant Interpretation Working Group. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from …

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Druggable genomic landscapes of high-grade gliomas D

Ghanem P, Fatteh M, Kamson DO, Balan A, Chang M, Tao J, Blakeley J; Johns Hopkins Molecular Tumor Board Investigators; Canzoniero J, Grossman SA, Marrone K, Schreck KC, Anagnostou V. Druggable genomic landscapes of high-grade gliomas. Front Med (Lausanne). 2023 Dec 8;10:1254955. doi: 10.3389/fmed.2023.1254955. PMID: 38143440; PMCID: PMC10749203.

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Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer C

Mistretta B, Rankothgedera S, Castillo M, Rao M, Holloway K, Bhardwaj A, El Noafal M, Albarracin C, El-Zein R, Rezaei H, Su X, Akbani R, Shao XM, Czerniecki BJ, Karchin R, Bedrosian I, Gunaratne PH. (2023) Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer. Front. Immunol. 2023 Sep 6:14:1188831

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Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity D

Albert BA, Yang Y, Shao XM, Singh D, Smith KN, Anagnostou V, Karchin R Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity (2023) Nat Mach Intell. https://doi.org/10.1038/s42256-023-00694-6

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Persistent mutation burden drives sustained anti-tumor immune responses P

Niknafs N, Balan A, Cherry C, Hummelink K, Monkhorst K, Shao XM, Belcaid Z, Marrone KA, Murray J, Smith KN, Levy B, Feliciano J, Hann CL, Lam V, Pardoll DM, Karchin R, Seiwert TY, Brahmer JR, Forde PM, Velculescu VE, Anagnostou V. (2023) Persistent mutation burden drives sustained anti-tumor immune responses. Nat Med. Feb;29(2):440-449

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Clustering by antigen-presenting genes reveals immune landscapes and predicts response to checkpoint immunotherapy C

Gong X, Karchin R (2023) Clustering by antigen-presenting genes reveals immune landscapes and predicts response to checkpoint immunotherapy Sci Rep. Jan 18;13(1):950

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