Schizophrenia and a high-resolution map of the three-dimensional chromatin interactome of adult and fetal cortex
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Yun Li | Yan Li | Danielle Posthuma | Yuchen Yang | Ming Hu | Leina Lu | Philip R Jansen | Patrick F Sullivan | Nenad Sestan | Ivan Juric | Fulai Jin | Michael J Owen | Gregory E Crawford | M. Owen | M. O’Donovan | P. Sullivan | G. Crawford | Yun Li | G. Rajkowska | D. Posthuma | N. Šestan | J. Crowley | Yan Li | Ming Hu | Fulai Jin | Joshua S. Martin | J. Savage | J. Bryois | J. Walters | A. Pardiñas | G. Santpere | P. Jansen | Sirisha Pochareddy | Cheynna A. Crowley | Yurae Shin | P. Giusti-Rodríguez | J. Overholser | C. Stockmeier | J. Guintivano | Yuchen Yang | G. Mahajan | G. Jurjus | Xiaoxiao Liu | Leina Lu | NaEshia Ancalade | Ivan Juric | Grazyna Rajkowska | George J Jurjus | Jerry Guintivano | Paola Giusti-Rodríguez | Xiaoxiao Liu | Antonio F Pardiñas | James T R Walters | Julien Bryois | Gabriel Santpere | Michael C O’Donovan | Jeanne E Savage | S. Allred | Cheynna A Crowley | Joshua S Martin | S. Colby Allred | NaEshia Ancalade | James J Crowley | Gouri Mahajan | James C Overholser | Sirisha Pochareddy | Yurae Shin | Craig A Stockmeier | Yun Li | S. C. Allred | N. Ancalade | Paola Giusti-Rodríguez | J. Walters
[1] T. Heskes,et al. The statistical properties of gene-set analysis , 2016, Nature Reviews Genetics.
[2] Peter H. L. Krijger,et al. Regulation of disease-associated gene expression in the 3D genome , 2016, Nature Reviews Molecular Cell Biology.
[3] Rachel Patton McCord,et al. Chromosome biology: How to build a cohesive genome in 3D , 2017, Nature.
[4] Nicola J. Rinaldi,et al. Genetic effects on gene expression across human tissues , 2017, Nature.
[5] J. Dostie,et al. Discovering genome regulation with 3C and 3C-related technologies. , 2012, Biochimica et biophysica acta.
[6] Erdogan Taskesen,et al. Functional mapping and annotation of genetic associations with FUMA , 2017, Nature Communications.
[7] B. Weir,et al. ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.
[8] Job Dekker,et al. Analysis of long-range chromatin interactions using Chromosome Conformation Capture. , 2012, Methods.
[9] D. Goldstein. Common genetic variation and human traits. , 2009, The New England journal of medicine.
[10] P. Visscher,et al. Rare chromosomal deletions and duplications increase risk of schizophrenia , 2008, Nature.
[11] Eric E Schadt,et al. A role for noncoding variation in schizophrenia. , 2014, Cell reports.
[12] M. Olivier. A haplotype map of the human genome. , 2003, Nature.
[13] M. Daly,et al. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies , 2014, Nature Genetics.
[14] Yan Li,et al. Easy Hi-C: A simple efficient protocol for 3D genome mapping in small cell populations , 2018, bioRxiv.
[15] E. Boerwinkle,et al. Ethnicity and human genetic linkage maps. , 2005, American journal of human genetics.
[16] Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .
[17] Josée Dostie,et al. From cells to chromatin: capturing snapshots of genome organization with 5C technology. , 2012, Methods.
[18] Darren J. Burgess,et al. Epigenomics: Deciphering non-coding variation with 3D epigenomics , 2016, Nature Reviews Genetics.
[19] J. Dekker,et al. Capturing Chromosome Conformation , 2002, Science.
[20] Minna Männikkö,et al. Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders , 2016, Nature Neuroscience.
[21] Evan Z. Macosko,et al. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types , 2017, Nature Genetics.
[22] Kyle J. Gaulton,et al. Detection of human adaptation during the past 2000 years , 2016, Science.
[23] Gabor T. Marth,et al. A global reference for human genetic variation , 2015, Nature.
[24] Simon C. Potter,et al. Genome-wide Association Analysis Identifies 14 New Risk Loci for Schizophrenia , 2013, Nature Genetics.
[25] Anthony D. Schmitt,et al. Genome-wide mapping and analysis of chromosome architecture , 2016, Nature Reviews Molecular Cell Biology.
[26] Jianxin Shi,et al. Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs , 2013, Nature Genetics.
[27] Y. Hurd,et al. An atlas of chromatin accessibility in the adult human brain , 2018, Genome research.
[28] Yang I Li,et al. An Expanded View of Complex Traits: From Polygenic to Omnigenic , 2017, Cell.
[29] Giacomo Cavalli,et al. Organization and function of the 3D genome , 2016, Nature Reviews Genetics.
[30] Benjamin A. Logsdon,et al. Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia , 2016, Nature Neuroscience.
[31] Raymond K. Auerbach,et al. A User's Guide to the Encyclopedia of DNA Elements (ENCODE) , 2011, PLoS biology.
[32] P. Donnelly,et al. A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome , 2005, Science.
[33] Gabor T. Marth,et al. An integrated map of structural variation in 2,504 human genomes , 2015, Nature.
[34] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[35] Warren W. Kretzschmar,et al. Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression , 2017, Nature Genetics.
[36] Bing Ren,et al. The Three-Dimensional Organization of Mammalian Genomes. , 2017, Annual review of cell and developmental biology.
[37] M C O'Donovan,et al. Copy number variation in schizophrenia in Sweden , 2014, Molecular Psychiatry.
[38] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[39] Sharon R Grossman,et al. Detecting natural selection in genomic data. , 2013, Annual review of genetics.
[40] Tanya M. Teslovich,et al. Discovery and refinement of loci associated with lipid levels , 2013, Nature Genetics.
[41] K. Pollard,et al. Most regulatory interactions are not in linkage disequilibrium , 2018, bioRxiv.
[42] Jakob Grove,et al. Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection , 2018, Nature Genetics.
[43] C. Spencer,et al. A contribution of novel CNVs to schizophrenia from a genome-wide study of 41,321 subjects: CNV Analysis Group and the Schizophrenia Working Group of the Psychiatric Genomics Consortium , 2016, bioRxiv.
[44] Y. Hurd,et al. The Genome in Three Dimensions: A New Frontier in Human Brain Research , 2014, Biological Psychiatry.
[45] Christopher S. Poultney,et al. Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci , 2015, Neuron.
[46] Eric S. Lander,et al. A polygenic burden of rare disruptive mutations in schizophrenia , 2014, Nature.
[47] N. Cox,et al. Obesity-associated variants within FTO form long-range functional connections with IRX3 , 2014, Nature.
[48] M. Jarvelin,et al. Deletion of TOP3β, a component of FMRP-containing mRNPs, contributes to neurodevelopmental disorders , 2013, Nature Neuroscience.
[49] Elvira Bramon,et al. Disruption of the neurexin 1 gene is associated with schizophrenia. , 2009, Human molecular genetics.
[50] V. Pirrotta. Binding the boundaries of chromatin domains , 2014, Genome Biology.
[51] Rob Patro,et al. Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.
[52] Stefan Schoenfelder,et al. Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci , 2015, Nature Communications.
[53] Tyrone D. Cannon,et al. Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence , 2018, Nature Genetics.
[54] S. Mundlos,et al. Breaking TADs: How Alterations of Chromatin Domains Result in Disease. , 2016, Trends in genetics : TIG.
[55] Nathan C. Sheffield,et al. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors , 2015, Nature Methods.
[56] Michael D. Cole,et al. Upregulation of c-MYC in cis through a Large Chromatin Loop Linked to a Cancer Risk-Associated Single-Nucleotide Polymorphism in Colorectal Cancer Cells , 2010, Molecular and Cellular Biology.
[57] Pavlos Pavlidis,et al. 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans , 2013, Nucleic Acids Res..
[58] William Stafford Noble,et al. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts , 2014, Genome research.
[59] P. Visscher,et al. Meta-analysis of genome-wide association studies for height and body mass index in ∼700,000 individuals of European ancestry , 2018, bioRxiv.
[60] Giulio Genovese,et al. Schizophrenia risk from complex variation of complement component 4 , 2016, Nature.
[61] Andrew Carroll,et al. Analysis commons, a team approach to discovery in a big-data environment for genetic epidemiology , 2017, Nature Genetics.
[62] Daning Lu,et al. Chromosome conformation elucidates regulatory relationships in developing human brain , 2016, Nature.
[63] Carl Kingsford,et al. Higher-order chromatin domains link eQTLs with the expression of far-away genes , 2013, Nucleic acids research.
[64] Gerome Breen,et al. Genetic identification of brain cell types underlying schizophrenia , 2017, Nature Genetics.
[65] M. Daly,et al. An Atlas of Genetic Correlations across Human Diseases and Traits , 2015, Nature Genetics.
[66] Alan M. Kwong,et al. A reference panel of 64,976 haplotypes for genotype imputation , 2015, Nature Genetics.
[67] Zheng Xu,et al. FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data , 2016, Bioinform..
[68] Anthony D. Schmitt,et al. A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. , 2016, Cell reports.
[69] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[70] Han Xu,et al. Partitioning heritability by functional category using GWAS summary statistics , 2015, bioRxiv.
[71] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[72] Giulio Genovese,et al. Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia , 2016, Nature Neuroscience.
[73] J. Dekker,et al. Chromosome Conformation Capture Carbon Copy Technology , 2007, Current protocols in molecular biology.
[74] Philip L. F. Johnson,et al. A Draft Sequence of the Neandertal Genome , 2010, Science.
[75] Yan Li,et al. A high-resolution map of three-dimensional chromatin interactome in human cells , 2013, Nature.
[76] K. Holsinger,et al. Genetics in geographically structured populations: defining, estimating and interpreting FST , 2009, Nature Reviews Genetics.
[77] M. Robinson,et al. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. , 2015, F1000Research.
[78] Terrence S. Furey,et al. A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data , 2016, Bioinform..
[79] Daniel R. Schrider,et al. Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome , 2016, bioRxiv.
[80] J. Dekker,et al. Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation , 2015, Nature.
[81] Stephen C. J. Parker,et al. The genetic architecture of type 2 diabetes , 2016, Nature.
[82] H. Stefánsson,et al. Truncating mutations in RBM12 are associated with psychosis , 2017, Nature Genetics.
[83] P. Visscher,et al. 10 Years of GWAS Discovery: Biology, Function, and Translation. , 2017, American journal of human genetics.
[84] Jennifer K Inlow,et al. Molecular and comparative genetics of mental retardation. , 2004, Genetics.
[85] Timothy E. Reddy,et al. Evaluation of Chromatin Accessibility in Prefrontal Cortex of Schizophrenia Cases and Controls , 2017, bioRxiv.
[86] Ming Hu,et al. HiCNorm: removing biases in Hi-C data via Poisson regression , 2012, Bioinform..
[87] K. Brennand,et al. Spatial genome organization and cognition , 2016, Nature Reviews Neuroscience.
[88] Job Dekker,et al. Mapping the 3D genome: Aiming for consilience , 2016, Nature Reviews Molecular Cell Biology.
[89] Nuno A. Fonseca,et al. Two independent modes of chromatin organization revealed by cohesin removal , 2017, Nature.
[90] Job Dekker,et al. Determining spatial chromatin organization of large genomic regions using 5C technology. , 2009, Methods in molecular biology.
[91] M. King,et al. Schizophrenia: a common disease caused by multiple rare alleles , 2007, British Journal of Psychiatry.
[92] Gerome Breen,et al. Psychiatric Genomics: An Update and an Agenda , 2017, bioRxiv.
[93] Judy H. Cho,et al. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations , 2015, Nature Genetics.
[94] J. Pritchard,et al. A Map of Recent Positive Selection in the Human Genome , 2006, PLoS biology.
[95] A. Jeffreys,et al. Factors influencing recombination frequency and distribution in a human meiotic crossover hotspot. , 2005, Human molecular genetics.
[96] Montgomery Slatkin,et al. Linkage disequilibrium — understanding the evolutionary past and mapping the medical future , 2008, Nature Reviews Genetics.
[97] J. Sedat,et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.
[98] P. Sullivan,et al. Quantitative Analysis of Focused A-To-I RNA Editing Sites by Ultra-High-Throughput Sequencing in Psychiatric Disorders , 2012, PloS one.
[99] Job Dekker,et al. Gene Regulation in the Third Dimension , 2008, Science.
[100] J. Dekker,et al. The long-range interaction landscape of gene promoters , 2012, Nature.
[101] Hoang T. Nguyen,et al. Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders , 2017, Genome Medicine.
[102] P. Sullivan,et al. Schizophrenia as a complex trait: evidence from a meta-analysis of twin studies. , 2003, Archives of general psychiatry.
[103] R. Young,et al. Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.
[104] G. Coop,et al. A Population Genetic Signal of Polygenic Adaptation , 2013, PLoS genetics.
[105] Wei Cheng,et al. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects , 2016, Nature Genetics.
[106] Zhiping Weng,et al. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk , 2018, Science.
[107] Job Dekker,et al. My5C: web tools for chromosome conformation capture studies , 2009, Nature Methods.
[108] A. Quinlan. BEDTools: The Swiss‐Army Tool for Genome Feature Analysis , 2014, Current protocols in bioinformatics.
[109] David A. Orlando,et al. Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.
[110] Jun S. Liu,et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.
[111] Jonathan M. Cairns,et al. Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition , 2018, Cell reports.
[112] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[113] Frank Grosveld,et al. Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions , 2013, Nature Protocols.
[114] Steve Horvath,et al. WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.
[115] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[116] Howard Y. Chang,et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.
[117] V. McKusick. Mendelian Inheritance in Man and Its Online Version, OMIM , 2007, The American Journal of Human Genetics.
[118] Jesse M. Engreitz,et al. Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression , 2016, Nature Reviews Molecular Cell Biology.
[119] Sharon R Grossman,et al. Integrating common and rare genetic variation in diverse human populations , 2010, Nature.