Categories: Technology

A compendium of artificial deadly gene pairs outlined by intensive combinatorial pan-cancer CRISPR screening | Genome Biology

This web page was created programmatically, to learn the article in its unique location you’ll be able to go to the hyperlink bellow:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03737-w
and if you wish to take away this text from our website please contact us


  • Nijman SMB. Synthetic lethality: common rules, utility and detection utilizing genetic screens in human cells. FEBS Lett. 2011;585:1–6.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Prakash R, Zhang Y, Feng W, Jasin M. Homologous recombination and human well being: the roles of BRCA1, BRCA2, and related proteins. Cold Spring Harb Perspect Biol. 2015;7:a016600.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Farmer H, McCabe N, Lord CJ, Tutt ANJ, Johnson DA, Richardson TB, et al. Targeting the DNA restore defect in BRCA mutant cells as a therapeutic technique. Nature. 2005;434:917–21.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Langelier M-F, Lin X, Zha S, Pascal JM. Clinical PARP inhibitors allosterically induce PARP2 retention on DNA. Sci Adv. 2023;9:eadf7175.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dempster JM, Pacini C, Pantel S, Behan FM, Green T, Krill-Burger J, et al. Agreement between two giant pan-cancer CRISPR-Cas9 gene dependency knowledge units. Nat Commun. 2019;10:5817.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Boehm JS, Garnett MJ, Adams DJ, Francies HE, Golub TR, Hahn WC, et al. Cancer analysis wants a greater map. Nature. 2021;589:514–6.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kegel BD, Ryan CJ. Paralog dispensability shapes homozygous deletion patterns in tumor genomes. Mol Syst Biol. 2023;19:e11987.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kegel BD, Ryan CJ. Paralog buffering contributes to the variable essentiality of genes in most cancers cell strains. PLoS Genet. 2019;15:e1008466.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dede M, McLaughlin M, Kim E, Hart T. Multiplex enCas12a screens detect practical buffering amongst paralogs in any other case masked in monogenic Cas9 knockout screens. Genome Biol. 2020;21:262.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, et al. Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017;14:573–6.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thompson NA, Ranzani M, van der Weyden L, Iyer V, Offord V, Droop A, et al. Combinatorial CRISPR display identifies health results of gene paralogues. Nat Commun. 2021;12:1302.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Parrish PCR, Thomas JD, Gabel AM, Kamlapurkar S, Bradley RK, Berger AH. Discovery of artificial deadly and tumor suppressor paralog pairs within the human genome. Cell Rep. 2021;36:109597.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gonatopoulos-Pournatzis T, Aregger M, Brown KR, Farhangmehr S, Braunschweig U, Ward HN, et al. Genetic interplay mapping and exon-resolution practical genomics with a hybrid Cas9–Cas12a platform. Nat Biotechnol. 2020;38:638–48.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ito T, Young MJ, Li R, Jain S, Wernitznig A, Krill-Burger JM, et al. Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers. Nat Genet. 2021;53:1664–72.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kegel BD, Quinn N, Thompson NA, Adams DJ, Ryan CJ. Comprehensive prediction of strong artificial lethality between paralog pairs in most cancers cell strains. Cell Syst. 2021;12:1144-1159.e6.

    Article 
    PubMed 

    Google Scholar
     

  • Ryan CJ, Mehta I, Kebabci N, Adams DJ. Targeting artificial deadly paralogs in most cancers. Trends Cancer. 2023;9:397–409.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Anvar NE, Lin C, Ma X, Wilson LL, Steger R, Sangree AK, et al. Efficient gene knockout and genetic interplay screening utilizing the in4mer CRISPR/Cas12a multiplex knockout platform. Nat Commun. 2024;15:3577.

    Article 

    Google Scholar
     

  • Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global most cancers statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 international locations. CA Cancer J Clin. 2021;71:209–49.

    PubMed 

    Google Scholar
     

  • Long GV, Swetter SM, Menzies AM, Gershenwald JE, Scolyer RA. Cutaneous melanoma. Lancet. 2023;402:485–502.

    Article 
    PubMed 

    Google Scholar
     

  • Lyne R, Smith R, Rutherford Ok, Wakeling M, Varley A, Guillier F, et al. FlyMine: an built-in database for Drosophila and Anopheles genomics. Genome Biol. 2007;8:R129–R129.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Davis P, Zarowiecki M, Arnaboldi V, Becerra A, Cain S, Chan J, et al. WormBase in 2022—knowledge, processes, and instruments for analyzing Caenorhabditis elegans. Genetics. 2022;220:iyac003.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thanki AS, Soranzo N, Haerty W, Davey RP. Geneseqtofamily: a Galaxy workflow to search out gene households primarily based on the Ensembl Compara GeneTrees. Gigascience. 2018;7:giy005.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Behan FM, Iorio F, Picco G, Gonçalves E, Beaver CM, Migliardi G, et al. Prioritization of most cancers therapeutic targets utilizing CRISPR–Cas9 screens. Nature. 2019;568:511–6.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cho H, Berger B, Peng J. Compact Integration of Multi-Network Topology for Functional Analysis of Genes. Cell Syst. 2016;3:540–548 e5. Available from: https://www.ncbi.nlm.nih.gov/pubmed/27889536

  • Chang Ok, Creighton CJ, Davis C, Donehower L, Drummond J, Wheeler D, et al. The Cancer Genome Atlas Pan-Cancer evaluation mission. Nat Genet. 2013;45:1113–20.

    Article 
    CAS 

    Google Scholar
     

  • Cheung HW, Cowley GS, Weir BA, Boehm JS, Rusin S, Scott JA, et al. Systematic investigation of genetic vulnerabilities throughout most cancers cell strains reveals lineage-specific dependencies in ovarian most cancers. Proc Natl Acad Sci U S A. 2011;108:12372–7.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barretina J, Caponigro G, Stransky N, Venkatesan Ok, Margolin AA, Kim S, et al. The most cancers cell line encyclopedia permits predictive modelling of anticancer drug sensitivity. Nature. 2012;483:603–7.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fortin J-P, Tan J, Gascoigne KE, Haverty PM, Forrest WF, Costa MR, et al. Multiple-gene concentrating on and mismatch tolerance can confound evaluation of genome-wide pooled CRISPR screens. Genome Biol. 2019;20:21.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Koike-Yusa H, Li Y, Tan E-P, Velasco-Herrera MDC, Yusa Ok. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol. 2013;32(3):267–73.

    Article 
    PubMed 

    Google Scholar
     

  • Morgens DW, Wainberg M, Boyle EA, Ursu O, Araya CL, Tsui CK, et al. Genome-scale measurement of off-target exercise utilizing Cas9 toxicity in high-throughput screens. Nat Commun. 2017;8:15178.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim E, Hart T. Improved evaluation of CRISPR health screens and lowered off-target results with the BAGEL2 gene essentiality classifier. Genome Med. 2021;13:2.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bliss CI. The toxicity of poisons utilized jointly1. Ann Appl Biol. 1939;26:585–615.

    Article 
    CAS 

    Google Scholar
     

  • Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, et al. MAGeCK permits strong identification of important genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 2014;15:554.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gökbağ B, Tang S, Fan Ok, Cheng L, Yu L, Zhao Y, et al. SLKB: artificial lethality data base. Nucleic Acids Res. 2023. https://doi.org/10.1093/nar/gkad806.

    Article 
    PubMed Central 

    Google Scholar
     

  • Köferle A, Schlattl A, Hörmann A, Spreitzer F, Popa A, Thatikonda V, et al. Interrogation of most cancers gene dependencies reveals novel paralog interactions of autosome and intercourse chromosome encoded genes. bioRxiv. 2021;39:2021.05.21.445116.

  • Malone CF, Dharia NV, Kugener G, Forman AB, Rothberg MV, Abdusamad M, et al. Selective modulation of a pan-essential protein as a therapeutic technique in most cancers. Cancer Discov. 2021;11:2282–99.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Krill-Burger JM, Dempster JM, Borah AA, Paolella BR, Root DE, Golub TR, et al. Partial gene suppression improves identification of most cancers vulnerabilities when CRISPR-Cas9 knockout is pan-lethal. Genome Biol. 2023;24:192.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, et al. The Genotype-Tissue Expression (GTEx) mission. Nat Genet. 2013;45:580–5.

    Article 
    CAS 

    Google Scholar
     

  • Consortium TIMP, Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, et al. Disease mannequin discovery from 3,328 gene knockouts by the International Mouse Phenotyping Consortium. Nat Genet. 2017;49:1231–8.

    Article 

    Google Scholar
     

  • Groza T, Gomez FL, Mashhadi HH, Muñoz-Fuentes V, Gunes O, Wilson R, et al. The International Mouse Phenotyping Consortium: complete knockout phenotyping underpinning the research of human illness. Nucleic Acids Res. 2022;51:D1038–45.

    Article 
    PubMed Central 

    Google Scholar
     

  • Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, et al. A genomic mutational constraint map utilizing variation in 76,156 human genomes. Nature. 2023;1–11.

  • Sondka Z, Dhir NB, Carvalho-Silva D, Jupe S, Madhumita, McLaren Ok, et al. COSMIC: a curated database of somatic variants and medical knowledge for most cancers. Nucleic Acids Res. 2023;52:D1210-7.

    Article 
    PubMed Central 

    Google Scholar
     

  • Kelleher KJ, Sheils TK, Mathias SL, Yang JJ, Metzger VT, Siramshetty VB, et al. Pharos 2023: an built-in useful resource for the understudied human proteome. Nucleic Acids Res. 2022;51:D1405–16.

    Article 
    PubMed Central 

    Google Scholar
     

  • Zorova LD, Popkov VA, Plotnikov EY, Silachev DN, Pevzner IB, Jankauskas SS, et al. Mitochondrial membrane potential. Anal Biochem. 2018;552:50–9.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Goldman MJ, Craft B, Hastie M, Repečka Ok, McDade F, Kamath A, et al. Visualizing and decoding most cancers genomics knowledge by way of the Xena platform. Nat Biotechnol. 2020;38:675–8.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Campbell PJ, Getz G, Korbel JO, Stuart JM, Jennings JL, Stein LD, et al. Pan-cancer evaluation of entire genomes. Nature. 2020;578:82–93.

    Article 

    Google Scholar
     

  • Tutt ANJ, Garber JE, Kaufman B, Viale G, Fumagalli D, Rastogi P, et al. Adjuvant olaparib for sufferers with BRCA1- or BRCA2-mutated breast most cancers. N Engl J Med. 2021;384:2394–405.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chan EM, Shibue T, McFarland JM, Gaeta B, Ghandi M, Dumont N, et al. WRN helicase is an artificial deadly goal in microsatellite unstable cancers. Nature. 2019;568:551–6.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Harle V, Offord V, Gökbağ B, Fotopoulos L, Williams T, Alexander D, Mehta I, Thompson NA, Olvera-León R, Peidli S, Iyer V, Gonçalves E, Kebabci N, de Kegel B, van de Haar J, Li L, Ryan C, Adams DJ. A compendium of artificial deadly gene pairs outlined by intensive combinatorial pan-cancer CRISPR screening. Zenodo. (2025).

  • Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, et al. Defining a most cancers dependency map. Cell. 2017;170:564-576.e16.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, et al. Assessing the importance of chromosomal aberrations in most cancers: methodology and utility to glioma. Proc Natl Acad Sci U S A. 2007;104:20007–12.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mohr SE, Hu Y, Kim Ok, Housden BE, Perrimon N. Resources for practical genomics research in Drosophila melanogaster. Genetics. 2014;197:1–18.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sanson KR, Hanna RE, Hegde M, Donovan KF, Strand C, Sullender ME, et al. Optimized libraries for CRISPR-Cas9 genetic screens with a number of modalities. Nat Commun. 2018;9:5416.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hart T, Tong AHY, Chan Ok, Leeuwen JV, Seetharaman A, Aregger M, et al. Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens. G3: Genes Genomes Genet. 2017;7:2719–27.

  • Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells utilizing the CRISPR-Cas9 system. Science. 2014;343:80–4.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chan PY, Alexander D, Mehta I, Matsuyama LSAS, Harle V, Olvera-León R, et al. The artificial deadly interplay between CDS1 and CDS2 is a vulnerability in uveal melanoma and throughout a number of tumor varieties. Nat Genet. 2025;57:1672–83.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vidigal JA, Ventura A. Rapid and environment friendly one-step technology of paired gRNA CRISPR-Cas9 libraries. Nat Commun. 2015;6:8083.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Masters JR. Cell-line authentication: finish the scandal of false cell strains. Nature. 2012;492:186.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tzelepis Ok, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, et al. A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia. Cell Rep. 2016;17:1193–205.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen Q, Chuai G, Zhang H, Tang J, Duan L, Guan H, et al. Genome-wide CRISPR off-target prediction and optimization utilizing RNA-DNA interplay fingerprints. Nat Commun. 2023;14:7521.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bae S, Park J, Kim J-S. Cas-OFFinder: a quick and versatile algorithm that searches for potential off-target websites of Cas9 RNA-guided endonucleases. Bioinformatics. 2014;30:1473–5.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, et al. DNA concentrating on specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013;31:827–32.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, et al. Optimized sgRNA design to maximise exercise and decrease off-target results of CRISPR-Cas9. Nat Biotechnol. 2016;34:184–91.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hoberecht L, Perampalam P, Lun A, Fortin J-P. A complete Bioconductor ecosystem for the design of CRISPR information RNAs throughout nucleases and applied sciences. Nat Commun. 2022;13:6568.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Benjamini Y, Hochberg Y. Controlling the false discovery charge: a sensible and highly effective method to a number of testing. J R Stat Soc Series B Stat Methodol. 1995;57:289–300.

    Article 

    Google Scholar
     

  • DepMap B. DepMap 24Q2 Public. 2024; Available from: https://plus.figshare.com/articles/dataset/DepMap_24Q2_Public/25880521

  • Harle V, Offord V, Gökbağ B, Fotopoulos L, Williams T, Alexander D, Mehta I, Thompson NA, Olvera-León R, Peidli S, Iyer V, Gonçalves E, Kebabci N, de Kegel B, van de Haar J, Li L, Ryan C, Adams DJ. A compendium of artificial deadly gene pairs outlined by intensive combinatorial pan-cancer CRISPR screening. Github. (2025).

  • Harle V, Offord V, Gökbağ B, Fotopoulos L, Williams T, Alexander D, Mehta I, Thompson NA, Olvera-León R, Peidli S, Iyer V, Gonçalves E, Kebabci N, de Kegel B, van de Haar J, Li L, Ryan C, Adams DJ. A compendium of artificial deadly gene pairs outlined by intensive combinatorial pan-cancer CRISPR screening. 2024. Figshare. https://doi.org/10.6084/m9.figshare.25954027.v4.

  • Harle V, Offord V, Gökbağ B, Fotopoulos L, Williams T, Alexander D, Mehta I, Thompson NA, Olvera-León R, Peidli S, Iyer V, Gonçalves E, Kebabci N, de Kegel B, van de Haar J, Li L, Ryan C, Adams DJ. A compendium of artificial deadly gene pairs outlined by intensive combinatorial pan-cancer CRISPR screening. ENA. (2023).

  • Harle V, Offord V, Gökbağ B, Fotopoulos L, Williams T, Alexander D, Mehta I, Thompson NA, Olvera-León R, Peidli S, Iyer V, Gonçalves E, Kebabci N, de Kegel B, van de Haar J, Li L, Ryan C, Adams DJ. A compendium of artificial deadly gene pairs outlined by intensive combinatorial pan-cancer CRISPR screening. EGA. https://ega-archive.org/datasets/EGAD00001003244 (2017).


  • This web page was created programmatically, to learn the article in its unique location you’ll be able to go to the hyperlink bellow:
    https://genomebiology.biomedcentral.com/articles/10.1186/s13059-025-03737-w
    and if you wish to take away this text from our website please contact us

    fooshya

    Recent Posts

    Methods to Fall Asleep Quicker and Keep Asleep, According to Experts

    This web page was created programmatically, to learn the article in its authentic location you…

    2 days ago

    Oh. What. Fun. film overview & movie abstract (2025)

    This web page was created programmatically, to learn the article in its unique location you…

    2 days ago

    The Subsequent Gaming Development Is… Uh, Controllers for Your Toes?

    This web page was created programmatically, to learn the article in its unique location you…

    2 days ago

    Russia blocks entry to US youngsters’s gaming platform Roblox

    This web page was created programmatically, to learn the article in its authentic location you…

    2 days ago

    AL ZORAH OFFERS PREMIUM GOLF AND LIFESTYLE PRIVILEGES WITH EXCLUSIVE 100 CLUB MEMBERSHIP

    This web page was created programmatically, to learn the article in its unique location you…

    2 days ago

    Treasury Targets Cash Laundering Community Supporting Venezuelan Terrorist Organization Tren de Aragua

    This web page was created programmatically, to learn the article in its authentic location you'll…

    2 days ago