Saturation variant interpretation using CRISPR prime editing

[1]  Simon P. Shen,et al.  Engineered pegRNAs improve prime editing efficiency , 2021, Nature Biotechnology.

[2]  Yulin Chen,et al.  Enhancing prime editing by Csy4-mediated processing of pegRNA , 2021, Cell Research.

[3]  Xiaoyue Wang,et al.  Identification of pathogenic variants in cancer genes using base editing screens with editing efficiency correction , 2021, Genome Biology.

[4]  T. Flotte,et al.  Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice , 2020, Nature Communications.

[5]  D. Nickerson,et al.  Multiplexed Functional Assessment of Genetic Variants in CARD11 , 2020, American journal of human genetics.

[6]  Jung-ki Yoon,et al.  Engineered prime editors with PAM flexibility , 2020, bioRxiv.

[7]  Sungroh Yoon,et al.  Predicting the efficiency of prime editing guide RNAs in human cells , 2020, Nature Biotechnology.

[8]  M. Firth,et al.  CRISPR GUARD protects off-target sites from Cas9 nuclease activity using short guide RNAs , 2020, Nature Communications.

[9]  David R. Liu,et al.  Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors , 2020, Nature Biotechnology.

[10]  David R. Liu,et al.  Massively parallel assessment of human variants with base editor screens , 2020, Cell.

[11]  Jian‐Kang Zhu,et al.  Precision genome engineering in rice using prime editing system , 2020, Plant biotechnology journal.

[12]  Benjamin P. Kleinstiver,et al.  Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants , 2020, Science.

[13]  Neo Christopher Chung,et al.  Statistical significance of cluster membership for unsupervised evaluation of cell identities , 2020, Bioinform..

[14]  R. Carrozzo,et al.  Molecular Genetics of Niemann–Pick Type C Disease in Italy: An Update on 105 Patients and Description of 18 NPC1 Novel Variants , 2020, Journal of clinical medicine.

[15]  R. Irizarry ggplot2 , 2019, Introduction to Data Science.

[16]  Gregory A. Newby,et al.  Search-and-replace genome editing without double-strand breaks or donor DNA , 2019, Nature.

[17]  David R. Liu,et al.  Search-and-replace genome editing without double-strand breaks or donor DNA , 2019, Nature.

[18]  R. Cohn,et al.  Modelling Niemann-Pick disease type C in a human haploid cell line allows for patient variant characterization and clinical interpretation , 2019, bioRxiv.

[19]  Woochang Lee,et al.  A CRISPR-based base-editing screen for the functional assessment of BRCA1 variants , 2019, Oncogene.

[20]  Kornel Labun,et al.  CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing , 2019, Nucleic Acids Res..

[21]  Douglas M. Fowler,et al.  Suppression of unwanted CRISPR-Cas9 editing by co-administration of catalytically inactivating truncated guide RNAs , 2019, Nature Communications.

[22]  Atina G. Coté,et al.  A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase , 2018, Genome Medicine.

[23]  Gregory M. Cooper,et al.  CADD: predicting the deleteriousness of variants throughout the human genome , 2018, Nucleic Acids Res..

[24]  Joseph D. Janizek,et al.  Accurate classification of BRCA1 variants with saturation genome editing , 2018, Nature.

[25]  John R. Garbe,et al.  EditR: A Method to Quantify Base Editing from Sanger Sequencing , 2018, The CRISPR journal.

[26]  David R. Liu,et al.  Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction , 2018, Nature Biotechnology.

[27]  Maitreya J. Dunham,et al.  Variant Interpretation: Functional Assays to the Rescue. , 2017, American journal of human genetics.

[28]  W. Chung,et al.  Risks of Breast, Ovarian, and Contralateral Breast Cancer for BRCA1 and BRCA2 Mutation Carriers , 2017, JAMA.

[29]  Raymond M. Moore,et al.  Comprehensive annotation of BRCA1 and BRCA2 missense variants by functionally validated sequence-based computational prediction models , 2017, Genetics in Medicine.

[30]  J. Shendure,et al.  Genome sequencing in a case of Niemann–Pick type C , 2016, Cold Spring Harbor molecular case studies.

[31]  Inês Barroso,et al.  Prospective functional classification of all possible missense variants in PPARG , 2016, Nature Genetics.

[32]  Marc Tessier-Lavigne,et al.  Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9 , 2016, Nature.

[33]  Gregory M. Cooper Parlez-vous VUS? , 2015, Genome research.

[34]  R. Marschalek,et al.  Optimized Sleeping Beauty transposons rapidly generate stable transgenic cell lines. , 2015, Biotechnology journal.

[35]  C. Greenberg,et al.  A rare case of Niemann–Pick disease type C without neurological involvement in a 66-year-old patient , 2015, Molecular genetics and metabolism reports.

[36]  C. Ponting,et al.  High Incidence of Unrecognized Visceral/Neurological Late-onset Niemann-Pick Disease, type C1 Predicted by Analysis of Massively Parallel Sequencing Data Sets , 2015, Genetics in Medicine.

[37]  Yao-Cheng Lin,et al.  Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations , 2014, Nature Communications.

[38]  S. Fields,et al.  Deep mutational scanning: a new style of protein science , 2014, Nature Methods.

[39]  Jay Shendure,et al.  Saturation Editing of Genomic Regions by Multiplex Homology-Directed Repair , 2014, Nature.

[40]  Jia Luo,et al.  Genome-wide identification of CRISPR/Cas9 off-targets in human genome , 2014, Cell Research.

[41]  David A. Scott,et al.  Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells , 2014, Nature Biotechnology.

[42]  Anneliese O. Speak,et al.  Relative acidic compartment volume as a lysosomal storage disorder-associated biomarker. , 2014, The Journal of clinical investigation.

[43]  Wei Zheng,et al.  A Phenotypic Compound Screening Assay for Lysosomal Storage Diseases , 2014, Journal of biomolecular screening.

[44]  David A. Scott,et al.  Genome engineering using the CRISPR-Cas9 system , 2013, Nature Protocols.

[45]  Eli J. Fine,et al.  DNA targeting specificity of RNA-guided Cas9 nucleases , 2013, Nature Biotechnology.

[46]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[47]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[48]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[49]  Carla P. Guimarães,et al.  Haploid Genetic Screens in Human Cells Identify Host Factors Used by Pathogens , 2009, Science.

[50]  S. Gale,et al.  Niemann-Pick Type C1 I1061T Mutant Encodes a Functional Protein That Is Selected for Endoplasmic Reticulum-associated Degradation Due to Protein Misfolding* , 2008, Journal of Biological Chemistry.

[51]  N. Baumann,et al.  The adult form of Niemann-Pick disease type C. , 2006, Brain : a journal of neurology.

[52]  G. Millat,et al.  Niemann-Pick C disease: use of denaturing high performance liquid chromatography for the detection of NPC1 and NPC2 genetic variations and impact on management of patients and families. , 2005, Molecular genetics and metabolism.

[53]  A Ralph Henderson,et al.  The bootstrap: a technique for data-driven statistics. Using computer-intensive analyses to explore experimental data. , 2005, Clinica chimica acta; international journal of clinical chemistry.

[54]  R. Dwek,et al.  Treatment with miglustat reverses the lipid-trafficking defect in Niemann–Pick disease type C , 2004, Neurobiology of Disease.

[55]  Susan L Neuhausen,et al.  Bilateral prophylactic mastectomy reduces breast cancer risk in BRCA1 and BRCA2 mutation carriers: the PROSE Study Group. , 2004, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[56]  O. Olopade,et al.  Efficacy of Risk‐Reducing Salpingo‐Oophorectomy in Women with BRCA‐1 and BRCA‐2 Mutations , 2004, The breast journal.

[57]  Dorin Comaniciu,et al.  Mean Shift: A Robust Approach Toward Feature Space Analysis , 2002, IEEE Trans. Pattern Anal. Mach. Intell..

[58]  C. Tomasetto,et al.  Niemann-Pick C1 disease: correlations between NPC1 mutations, levels of NPC1 protein, and phenotypes emphasize the functional significance of the putative sterol-sensing domain and of the cysteine-rich luminal loop. , 2001, American journal of human genetics.

[59]  H. Ninomiya,et al.  [Niemann-Pick disease type C]. , 2001, Nihon rinsho. Japanese journal of clinical medicine.

[60]  G. Millat,et al.  Niemann-Pick C1 disease: the I1061T substitution is a frequent mutant allele in patients of Western European descent and correlates with a classic juvenile phenotype. , 1999, American journal of human genetics.

[61]  M. Dobson,et al.  Mutations in NPC1 highlight a conserved NPC1-specific cysteine-rich domain. , 1999, American journal of human genetics.

[62]  H. Watari,et al.  Mutations in the Leucine Zipper Motif and Sterol-sensing Domain Inactivate the Niemann-Pick C1 Glycoprotein* , 1999, The Journal of Biological Chemistry.

[63]  J. Kopitz,et al.  [14C]Methylamine accumulation in cultured human skin fibroblasts--a biochemical test for lysosomal storage and lysosomal diseases. , 1994, Clinica chimica acta; international journal of clinical chemistry.

[64]  B. Bembi,et al.  Treatment of Human Fibroblasts Carrying NPC1 Missense Mutations with MG132 Leads to an Improvement of Intracellular Cholesterol Trafficking. , 2012, JIMD reports.