Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation

The promise and challenge of therapeutic genome editing

(2020) Jennifer A. Doudna   NATURE

Continuous evolution of SpCas9 variants compatible with non-G PAMs

(2020) Shannon M. Miller et al.   NATURE BIOTECHNOLOGY

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

(2020) Kailong Li et al.   Nature Communications

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

(2020) John P. Ray et al.   Nature Communications

A practical view of fine-mapping and gene prioritization in the post-genome-wide association era

(2020) R. V. Broekema et al.   Open Biology

Regulatory mechanisms of major depressive disorder risk variants

(2020) Shiwu Li et al.   MOLECULAR PSYCHIATRY

A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing

(2020) Julian Grünewald et al.   NATURE BIOTECHNOLOGY

Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease

(2020) Julien Bryois et al.   NATURE GENETICS

Therapeutic base editing of human hematopoietic stem cells

(2020) Jing Zeng et al.   NATURE MEDICINE

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Multiplexed CRISPR technologies for gene editing and transcriptional regulation

(2020) Nicholas S. McCarty et al.   Nature Communications

From GWAS to Function: Using Functional Genomics to Identify the Mechanisms Underlying Complex Diseases

(2020) Eddie Cano-Gamez et al.   Frontiers in Genetics

CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells

(2020) Ibrahim C. Kurt et al.   NATURE BIOTECHNOLOGY

Glycosylase base editors enable C-to-A and C-to-G base changes

(2020) Dongdong Zhao et al.   NATURE BIOTECHNOLOGY

Targeted, efficient sequence insertion and replacement in rice

(2020) Yuming Lu et al.   NATURE BIOTECHNOLOGY

The Polygenic and Monogenic Basis of Blood Traits and Diseases

(2020) Dragana Vuckovic et al.   CELL

Predicting the efficiency of prime editing guide RNAs in human cells

(2020) Hui Kwon Kim et al.   NATURE BIOTECHNOLOGY

Post-Transcriptional Genetic Silencing of BCL11A to Treat Sickle Cell Disease

(2020) Erica B. Esrick et al.   NEW ENGLAND JOURNAL OF MEDICINE

Highly efficient therapeutic gene editing of human hematopoietic stem cells

(2019) Yuxuan Wu et al.   NATURE MEDICINE

Interrogation of human hematopoiesis at single-cell and single-variant resolution

(2019) Jacob C. Ulirsch et al.   NATURE GENETICS

CasX enzymes comprise a distinct family of RNA-guided genome editors

(2019) Jun-Jie Liu et al.   NATURE

Evaluating and Enhancing Target Specificity of Gene-Editing Nucleases and Deaminases

(2019) Daesik Kim et al.   Annual Review of Biochemistry

Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9

(2019) S. Ali Shariati et al.   MOLECULAR CELL

Benefits and limitations of genome-wide association studies

(2019) Vivian Tam et al.   NATURE REVIEWS GENETICS

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Chromatin three-dimensional interactions mediate genetic effects on gene expression

(2019) O. Delaneau et al.   SCIENCE

CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical Applications

(2019) Kutubuddin A. Molla et al.   TRENDS IN BIOTECHNOLOGY

Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells

(2019) Ryan T. Leenay et al.   NATURE BIOTECHNOLOGY

High-throughput identification of human SNPs affecting regulatory element activity

(2019) Joris van Arensbergen et al.   NATURE GENETICS

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

(2019) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Chromatin activity at GWAS loci identifies T cell states driving complex immune diseases

(2019) Blagoje Soskic et al.   NATURE GENETICS

Synergistic effects of common schizophrenia risk variants

(2019) Nadine Schrode et al.   NATURE GENETICS

Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms

(2019) Rebecca L. Walker et al.   CELL

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

(2019) Alexi Nott et al.   SCIENCE

Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

(2019) Martin Kircher et al.   Nature Communications

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements

(2019) Josh Tycko et al.   Nature Communications

Advances in genome editing through control of DNA repair pathways

(2019) Charles D. Yeh et al.   NATURE CELL BIOLOGY

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Deciphering Gene Regulation Using Massively Parallel Reporter Assays

(2019) Max Trauernicht et al.   TRENDS IN BIOCHEMICAL SCIENCES

Strategies for the CRISPR-Based Therapeutics

(2019) Bin Li et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

The Post-GWAS Era: From Association to Function

(2018) Michael D. Gallagher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation

(2018) Xiao-Feng Chen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2018) Ryan Tewhey et al.   CELL

Main steps in DNA double-strand break repair: an introduction to homologous recombination and related processes

(2018) Lepakshi Ranjha et al.   CHROMOSOMA

Synthesis-dependent repair of Cpf1-induced double strand DNA breaks enables targeted gene replacement in rice

(2018) Shaoya Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein

(2018) Winston X. Yan et al.   MOLECULAR CELL

High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction

(2018) Gang Li et al.   NATURE GENETICS

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

(2018) Hilary K. Finucane et al.   NATURE GENETICS

p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells

(2018) Robert J. Ihry et al.   NATURE MEDICINE

An enhanced CRISPR repressor for targeted mammalian gene regulation

(2018) Nan Cher Yeo et al.   NATURE METHODS

From genome-wide associations to candidate causal variants by statistical fine-mapping

(2018) Daniel J. Schaid et al.   NATURE REVIEWS GENETICS

Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

(2018) Matthew M. Makowski et al.   Nature Communications

Identification of Functional Variants in the FAM13A COPD GWAS Locus by Massively Parallel Reporter Assays

(2018) Peter J Castaldi et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Accurate classification of BRCA1 variants with saturation genome editing

(2018) Gregory M. Findlay et al.   NATURE

CRISPR-Cas guides the future of genetic engineering

(2018) Gavin J. Knott et al.   SCIENCE

Engineered CRISPR-Cas9 nuclease with expanded targeting space

(2018) Hiroshi Nishimasu et al.   SCIENCE

Deciphering the Emerging Complexities of Molecular Mechanisms at GWAS Loci

(2018) Maren E. Cannon et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Predictable and precise template-free CRISPR editing of pathogenic variants

(2018) Max W. Shen et al.   NATURE

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

(2018) Natsuhiko Kumasaka et al.   NATURE GENETICS

High prevalence of Streptococcus pyogenes Cas9-reactive T cells within the adult human population

(2018) Dimitrios L. Wagner et al.   NATURE MEDICINE

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics

(2018) Matthew D. Krause et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

(2017) Shiqi Xie et al.   MOLECULAR CELL

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

(2017) Gaelen T. Hess et al.   MOLECULAR CELL

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci

(2017) Matthew C Canver et al.   NATURE GENETICS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Optimizing the DNA Donor Template for Homology-Directed Repair of Double-Strand Breaks

(2017) Fei Song et al.   Molecular Therapy-Nucleic Acids

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

(2016) Jacob C. Ulirsch et al.   CELL

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

(2016) Angelo Amabile et al.   CELL

The Genetics of Transcription Factor DNA Binding Variation

(2016) Bart Deplancke et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans

(2016) Yang Li et al.   CELL

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

(2016) Frank Soldner et al.   NATURE

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes

(2016) David W Morgens et al.   NATURE BIOTECHNOLOGY

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes

(2016) André Mateus et al.   Proteome Science

RNA splicing is a primary link between genetic variation and disease

(2016) Yang I. Li et al.   SCIENCE

Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer

(2016) Steffen Grampp et al.   Nature Communications

The Rheumatoid Arthritis Risk Variant CCR6DNP Regulates CCR6 via PARP-1

(2016) Gang Li et al.   PLoS Genetics

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol

(2015) Tamara S. Roman et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort

(2015) Christopher M. Vockley et al.   GENOME RESEARCH

Induced Pluripotent Stem Cells

(2015) Kitchener D. Wilson et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

A light-inducible CRISPR-Cas9 system for control of endogenous gene activation

(2015) Lauren R Polstein et al.   Nature Chemical Biology

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

Therapeutic genome editing: prospects and challenges

(2015) David Benjamin Turitz Cox et al.   NATURE MEDICINE

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1

(2015) Cong Guo et al.   Nature Communications

Biological interpretation of genome-wide association studies using predicted gene functions

(2015) Tune H. Pers et al.   Nature Communications

SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci

(2014) Kamil Slowikowski et al.   BIOINFORMATICS

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Characterization of the transcriptional machinery bound across the widely presumed type 2 diabetes causal variant, rs7903146, within TCF7L2

(2014) Qianghua Xia et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding

(2014) Qilai Huang et al.   NATURE GENETICS

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery

(2014) Steven Lin et al.   eLife

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

(2013) O. Corradin et al.   GENOME RESEARCH

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level

(2013) D. E. Bauer et al.   SCIENCE

Meta-analysis of 2040 sickle cell anemia patients: BCL11A and HBS1L-MYB are the major modifiers of HbF in African Americans

(2012) H. T. Bae et al.   BLOOD

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia

(2012) Vijay G. Sankaran et al.   JOURNAL OF CLINICAL INVESTIGATION

Playing the End Game: DNA Double-Strand Break Repair Pathway Choice

(2012) J. Ross Chapman et al.   MOLECULAR CELL

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Integrating Autoimmune Risk Loci with Gene-Expression Data Identifies Specific Pathogenic Immune Cell Subsets

(2011) Xinli Hu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease

(2011) Heribert Schunkert et al.   NATURE GENETICS

LocusZoom: regional visualization of genome-wide association scan results

(2010) R. J. Pruim et al.   BIOINFORMATICS

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   CELL

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

(2010) Josiane E. Garneau et al.   NATURE

Determining the specificity of protein–DNA interactions

(2010) Gary D. Stormo et al.   NATURE REVIEWS GENETICS

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Proteomics strategy for quantitative protein interaction profiling in cell extracts

(2009) Kirti Sharma et al.   NATURE METHODS

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

Multiple Genetic Loci for Bone Mineral Density and Fractures

(2008) Unnur Styrkarsdottir et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of  -thalassemia

(2008) M. Uda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings

(2008) Mitch McVey et al.   TRENDS IN GENETICS