Data and analyses associated with CAVA
CAVA_prioritization_master_list.csv was generated by gathering data for each gene on the number of VUS and known pathogenic and benign variants from ClinVar(1) and the number of registered genetic tests from NIH Genetic Test Registry(2). We also curated data from several other sources included the Global Protein Stability screen where ~8,000 proteins were overexpressed with GFP tags(3), the Meltome Atlas which measured proteome-wide protein stability(4) and screens for gene essentiality in HAP1 and B cells(5, 6).
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M. J. Landrum, J. M. Lee, G. R. Riley, W. Jang, W. S. Rubinstein, D. M. Church, D. R. Maglott, ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 42, D980–5 (2014).
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W. S. Rubinstein, D. R. Maglott, J. M. Lee, B. L. Kattman, A. J. Malheiro, M. Ovetsky, V. Hem, V. Gorelenkov, G. Song, C. Wallin, N. Husain, S. Chitipiralla, K. S. Katz, D. Hoffman, W. Jang, M. Johnson, F. Karmanov, A. Ukrainchik, M. Denisenko, C. Fomous, K. Hudson, J. M. Ostell, The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency. Nucleic Acids Res. 41, D925–35 (2013).
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H.-C. S. Yen, Q. Xu, D. M. Chou, Z. Zhao, S. J. Elledge, Global protein stability profiling in mammalian cells. Science. 322, 918–923 (2008).
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A. Jarzab, N. Kurzawa, T. Hopf, M. Moerch, J. Zecha, N. Leijten, Y. Bian, E. Musiol, M. Maschberger, G. Stoehr, I. Becher, C. Daly, P. Samaras, J. Mergner, B. Spanier, A. Angelov, T. Werner, M. Bantscheff, M. Wilhelm, M. Klingenspor, S. Lemeer, W. Liebl, H. Hahne, M. M. Savitski, B. Kuster, Meltome atlas-thermal proteome stability across the tree of life. Nat. Methods. 17, 495–503 (2020).
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V. A. Blomen, P. Májek, L. T. Jae, J. W. Bigenzahn, J. Nieuwenhuis, J. Staring, R. Sacco, F. R. van Diemen, N. Olk, A. Stukalov, C. Marceau, H. Janssen, J. E. Carette, K. L. Bennett, J. Colinge, G. Superti-Furga, T. R. Brummelkamp, Gene essentiality and synthetic lethality in haploid human cells. Science. 350, 1092–1096 (2015).
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J. D. Phelan, R. M. Young, D. E. Webster, S. Roulland, G. W. Wright, M. Kasbekar, A. L. Shaffer 3rd, M. Ceribelli, J. Q. Wang, R. Schmitz, M. Nakagawa, E. Bachy, D. W. Huang, Y. Ji, L. Chen, Y. Yang, H. Zhao, X. Yu, W. Xu, M. M. Palisoc, R. R. Valadez, T. Davies-Hill, W. H. Wilson, W. C. Chan, E. S. Jaffe, R. D. Gascoyne, E. Campo, A. Rosenwald, G. Ott, J. Delabie, L. M. Rimsza, F. J. Rodriguez, F. Estephan, M. Holdhoff, M. J. Kruhlak, S. M. Hewitt, C. J. Thomas, S. Pittaluga, T. Oellerich, L. M. Staudt, A multiprotein supercomplex controlling oncogenic signalling in lymphoma. Nature. 560, 387–391 (2018).