A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

[1]  Gabor T. Marth,et al.  An integrated map of structural variation in 2,504 human genomes , 2015, Nature.

[2]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[3]  Alexander Schönhuth,et al.  Repeat- and error-aware comparison of deletions , 2015, Bioinform..

[4]  Tom R. Gaunt,et al.  The UK10K project identifies rare variants in health and disease , 2016 .

[5]  Bradley P. Coe,et al.  Global diversity, population stratification, and selection of human copy-number variation , 2015, Science.

[6]  Alan M. Kwong,et al.  Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers , 2015, Nature Genetics.

[7]  Siu-Ming Yiu,et al.  Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2015, GigaScience.

[8]  C. Wijmenga,et al.  Population-specific genotype imputations using minimac or IMPUTE2 , 2015, Nature Protocols.

[9]  Dan Nettleton,et al.  SimSeq: a nonparametric approach to simulation of RNA-sequence datasets , 2015, Bioinform..

[10]  Alexander Schönhuth,et al.  Characteristics of de novo structural changes in the human genome , 2015, Genome research.

[11]  Morris Swertz,et al.  Genome-wide patterns and properties of de novo mutations in humans , 2015, Nature Genetics.

[12]  James T. Elder,et al.  eQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues , 2015, Nature Communications.

[13]  Jakob Grove,et al.  Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios , 2015, Nature Communications.

[14]  Yufeng Wu,et al.  GINDEL: Accurate Genotype Calling of Insertions and Deletions from Low Coverage Population Sequence Reads , 2014, PloS one.

[15]  Mark J. P. Chaisson,et al.  Resolving the complexity of the human genome using single-molecule sequencing , 2014, Nature.

[16]  Kai Ye,et al.  Mobster: accurate detection of mobile element insertions in next generation sequencing data , 2014, Genome Biology.

[17]  Pieter B. T. Neerincx,et al.  Supplementary Information Whole-genome sequence variation , population structure and demographic history of the Dutch population , 2022 .

[18]  Heorhiy Byelas,et al.  Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands' , 2014, European Journal of Human Genetics.

[19]  Iman Hajirasouliha,et al.  MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels , 2013, Bioinform..

[20]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[21]  Lars Feuk,et al.  The Database of Genomic Variants: a curated collection of structural variation in the human genome , 2013, Nucleic Acids Res..

[22]  Jean-François Zagury,et al.  Haplotype estimation using sequencing reads. , 2013, American journal of human genetics.

[23]  Pieter B. T. Neerincx,et al.  The Genome of the Netherlands: design, and project goals , 2013, European Journal of Human Genetics.

[24]  Li Ding,et al.  Retrotransposition of gene transcripts leads to structural variation in mammalian genomes , 2013, Genome Biology.

[25]  Stephan Ripke,et al.  Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies. , 2013, The American journal of psychiatry.

[26]  Peng Chen,et al.  Deep whole-genome sequencing of 100 southeast Asian Malays. , 2013, American journal of human genetics.

[27]  Matthew W. Hahn,et al.  Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans , 2013, PLoS genetics.

[28]  Jian Wang,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[29]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[30]  David C. Wilson,et al.  Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease , 2012, Nature.

[31]  Shane J. Neph,et al.  Systematic Localization of Common Disease-Associated Variation in Regulatory DNA , 2012, Science.

[32]  V. Beneš,et al.  DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..

[33]  Lovelace J. Luquette,et al.  Landscape of Somatic Retrotransposition in Human Cancers , 2012, Science.

[34]  Alexander Schliep,et al.  CLEVER: clique-enumerating variant finder , 2012, Bioinform..

[35]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[36]  O. Delaneau,et al.  A linear complexity phasing method for thousands of genomes , 2011, Nature Methods.

[37]  Carlos S. Moreno,et al.  Relative Burden of Large CNVs on a Range of Neurodevelopmental Phenotypes , 2011, PLoS genetics.

[38]  Adrian M. Stütz,et al.  A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans , 2011, PLoS genetics.

[39]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[40]  M. Gerstein,et al.  CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. , 2011, Genome research.

[41]  Deniz Yorukoglu,et al.  Alu repeat discovery and characterization within human genomes. , 2011, Genome research.

[42]  Markus J. van Roosmalen,et al.  Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. , 2011, Human molecular genetics.

[43]  Joshua M. Korn,et al.  Discovery and genotyping of genome structural polymorphism by sequencing on a population scale , 2011, Nature Genetics.

[44]  Tariq Ahmad,et al.  Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci , 2010, Nature Genetics.

[45]  Sharon R Grossman,et al.  Integrating common and rare genetic variation in diverse human populations , 2010, Nature.

[46]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[47]  J. Marchini,et al.  Genotype imputation for genome-wide association studies , 2010, Nature Reviews Genetics.

[48]  Daniel Rios,et al.  Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .

[49]  Bradley P. Coe,et al.  FACADE: a fast and sensitive algorithm for the segmentation and calling of high resolution array CGH data , 2010, Nucleic acids research.

[50]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[51]  Tomas W. Fitzgerald,et al.  Origins and functional impact of copy number variation in the human genome , 2010, Nature.

[52]  Yong-shu He,et al.  [Structural variation in the human genome]. , 2009, Yi chuan = Hereditas.

[53]  Ian H. Witten,et al.  The WEKA data mining software: an update , 2009, SKDD.

[54]  R. Wilson,et al.  BreakDancer: An algorithm for high resolution mapping of genomic structural variation , 2009, Nature Methods.

[55]  Kai Ye,et al.  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..

[56]  P. Donnelly,et al.  A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies , 2009, PLoS genetics.

[57]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[58]  Erik Sistermans,et al.  Genomic microarrays in mental retardation: A practical workflow for diagnostic applications , 2009, Human mutation.

[59]  Gonçalo Abecasis,et al.  Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis , 2009, Nature Genetics.

[60]  B. J. Klevering,et al.  Identification of a 2 Mb human ortholog of Drosophila eyes shut/spacemaker that is mutated in patients with retinitis pigmentosa. , 2008, American journal of human genetics.

[61]  Matthew E Hurles,et al.  The functional impact of structural variation in humans. , 2008, Trends in genetics : TIG.

[62]  Philippe Froguel,et al.  FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity , 2007, Nature Genetics.

[63]  R. Redon,et al.  Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes , 2007, Science.

[64]  Ryan E. Mills,et al.  An initial map of insertion and deletion (INDEL) variation in the human genome. , 2006, Genome research.

[65]  Zhaohui S. Qin,et al.  A comparison of phasing algorithms for trios and unrelated individuals. , 2006, American journal of human genetics.

[66]  Toshihiro Tanaka The International HapMap Project , 2003, Nature.

[67]  Whole-genome sequence variation , population structure and demographic history of the Dutch population The Genome of the Netherlands Consortium * , 2014 .

[68]  Jonathan Marchini,et al.  Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold , 2013, Bioinform..

[69]  Sven Rahmann,et al.  Genome analysis , 2022 .

[70]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[71]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .