A machine learning algorithm with subclonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity von Pyke, Rachel Marty, Mellacheruvu, Dattatreya, Dea, Steven, Abbott, Charles W., McDaniel, Lee, Bhave, Devayani P., Zhang, Simo V., Levy, Eric, Bartha, Gabor, West, John, Snyder, Michael P., Chen, Richard O., Boyle, Sean Michael

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Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies von Waterhouse, Robert M, Aganezov, Sergey, Anselmetti, Yoann, Lee, Jiyoung, Ruzzante, Livio, Reijnders, Maarten J M F, Feron, Romain, Bérard, Sèverine, George, Phillip, Hahn, Matthew W, Howell, Paul I, Kamali, Maryam, Koren, Sergey, Lawson, Daniel, Maslen, Gareth, Peery, Ashley, Phillippy, Adam M, Sharakhova, Maria V, Tannier, Eric, Unger, Maria F, Zhang, Simo V, Alekseyev, Max A, Besansky, Nora J, Chauve, Cedric, Emrich, Scott J, Sharakhov, Igor V

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The sequencing and interpretation of the genome obtained from a Serbian individual von Mohammed Ismail, Wazim, Pagel, Kymberleigh A, Pejaver, Vikas, Zhang, Simo V, Casasa, Sofia, Mort, Matthew, Cooper, David N, Hahn, Matthew W, Radivojac, Predrag

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Prediction of Immunotherapy Response in Melanoma through Combined Modeling of Neoantigen Burden and Immune-Related Resistance Mechanisms von Abbott, Charles W, Boyle, Sean M, Pyke, Rachel Marty, McDaniel, Lee D, Levy, Eric, Navarro, Fábio C P, Mellacheruvu, Dattatreya, Zhang, Simo V, Tan, Mengyao, Santiago, Rose, Rusan, Zeid M, Milani, Pamela, Bartha, Gabor, Harris, Jason, McClory, Rena, Snyder, Michael P, Jang, Sekwon, Chen, Richard

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Precision Neoantigen Discovery Using Large-Scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation von Pyke, Rachel Marty, Mellacheruvu, Datta, Dea, Steven, Abbott, Charles, Zhang, Simo V., Phillips, Nick A., Harris, Jason, Bartha, Gabor, Desai, Sejal, McClory, Rena, West, John, Snyder, Michael P., Chen, Richard, Boyle, Sean Michael

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Intraspecific Genetic Variation Underlying Postmating Reproductive Barriers between Species in the Wild Tomato Clade (Solanum sect. Lycopersicon) von Jewell, Cathleen P, Zhang, Simo V, Gibson, Matthew J S, Tovar-Méndez, Alejandro, McClure, Bruce, Moyle, Leonie C

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Withdrawal of ‘Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation’ von Pyke, Rachel Marty, Mellacheruvu, Dattatreya, Dea, Steven, Abbott, Charles W., Zhang, Simo V., Phillips, Nick A., Harris, Jason, Bartha, Gabor, Desai, Sejal, McClory, Rena, West, John, Snyder, Michael P., Chen, Richard, Boyle, Sean Michael

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AGOUTI: improving genome assembly and annotation using transcriptome data von Zhang, Simo V, Zhuo, Luting, Hahn, Matthew W

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Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations von Hahn, Matthew W, Zhang, Simo V, Moyle, Leonie C

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Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation von Pyke, Rachel Marty, Mellacheruvu, Dattatreya, Dea, Steven, Abbott, Charles W., Zhang, Simo V., Phillips, Nick A., Harris, Jason, Bartha, Gabor, Desai, Sejal, McClory, Rena, West, John, Snyder, Michael P., Chen, Richard, Boyle, Sean Michael

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A pan-cancer profiling of somatic mutations and tumor microenvironment to reveal mutation dependent immunophenotypic signature differences in KRAS von McDaniel, Lee, Abbott, Charles, Pyke, Rachel, Levy, Eric, Zhang, Simo V., Wang, Jing, McClory, Rena, Chen, Richard, Boyle, Sean Michael

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Robust prediction of response to immunotherapy in a mixed cohort of previously treated and immunotherapy-naive melanoma patients von Abbott, Charles, McDaniel, Lee, Pyke, Rachel, Levy, Eric, Navarro, Fabio, Zhang, Simo V., Wang, Jing, McClory, Rena, Snyder, Michael, Jang, Sekwon, Boyle, Sean Michael, Chen, Richard

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Abstract 6678: Sensitive HLA loss of heterozygosity detection reveals allele-specific neoantigen expansion as resistance mechanism to anti-PD-1 therapy von Pyke, Rachel Marty, Abbott, Charles, Mellacheruvu, Dattatreya, Zhang, Simo V., Bedi, Nikita, Colevas, A. Dimitrios, Sunwoo, John, West, John, Chen, Richard, Boyle, Sean Michael

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Exome scale liquid biopsy characterization of putative neoantigens and genomic biomarkers pre- and post anti-PD-1 therapy in squamous cell carcinoma of the head and neck von Abbott, Charles, Bedi, Nikita, Zhang, Simo V, Li, Robin, Pyke, Rachel, Levy, Eric, Chernock, Rebecca, Mansour, Mena, Sunwoo, John B., Colevas, A. Dimitrios, Chen, Richard, Boyle, Sean Michael

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Abstract 399: Pan-cancer survey of HLA loss of heterozygosity using a robustly validated NGS-based machine learning algorithm von Pyke, Rachel Marty, Mellacheruvu, Datta, Abbott, Charles, Dea, Steven, Levy, Eric, Zhang, Simo V., Bedi, Nikita, Colevas, A. Dimitrios, Bhave, Devayani, Chinnappa, Manju, Bartha, Gabor, Lyle, John, West, John, Snyder, Michael, Sunwoo, John, Chen, Richard, Boyle, Sean Michael

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Abstract 555: Longitudinal exome-scale liquid biopsy monitoring of evolving therapeutic resistance mechanisms in head and neck squamous cell carcinoma patients receiving anti-PD-1... von Abbott, Charles W., Bedi, Nikita, Zhang, Simo V., Northcott, Josette, LI, Robin, Pyke, Rachel Marty, Levy, Eric, Chernock, Rebecca, Mansour, Mena, Colevas, A. Dimitrios, Lyle, John, Sunwoo, John B., Boyle, Sean, Chen, Richard

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Association of HLA loss of heterozygosity with allele-specific neoantigen expansion in response to immunotherapy von Pyke, Rachel Marty, Abbott, Charles, Dea, Steven, Bedi, Nikita, Colevas, A. Dimitrios, Levy, Eric, Zhang, Simo V., Snyder, Michael, Mellacheruvu, Datta, Sunwoo, John B., Chen, Richard, Boyle, Sean Michael

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Abstract 4695: Development and validation of an accurate exome-scale cfDNA detection platform von Zhang, Simo V., Abbott, Charles, Li, Robin, Levy, Eric, Luo, Shujun, Power, Robert, McClory, Rena, West, John, Chen, Richard, Boyle, Sean Michael

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Abstract 1989: Enhanced whole exome profiling of tumor circulating cell-free DNA enables sensitive assessment of tumor mutations von Zhang, Simo V., Tan, Mengyao, Northcott, Josette M., Ma, Shuyuan, Nelson, Christopher S., Bentley, L. Gordon, Chinnappa, Manju, Bhave, Devayani P., Norton, Dan, Harris, Jason, Boyle, Sean M., West, John, Chen, Richard

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Abstract A19: HLA allele-specific loss of heterozygosity detection using augmented exome capture approach von Pyke, Rachel Marty, Abbott, Charles, Zhang, Simo V., Mellacheruvu, Datta, West, John, Chen, Richard, Boyle, Sean Michael

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