Supplementary Information Whole-genome sequence variation , population structure and demographic history of the Dutch population
暂无分享,去创建一个
Pieter B. T. Neerincx | Jeroen F. J. Laros | David van Enckevort | A. Hofman | A. Uitterlinden | R. Handsaker | J. Hehir-Kwa | F. Hormozdiari | D. Cox | S. Mccarroll | C. Wijmenga | Jun Wang | Yingrui Li | M. Stoneking | I. Pe’er | Qibin Li | Ning Li | K. Ye | S. Sunyaev | F. Rivadeneira | C. Duijn | G. Willemsen | P. Polak | H. Cao | W. Kloosterman | J. Bovenberg | D. Boomsma | M. Swertz | T. Marschall | S. Pulit | J. Veldink | J. Hottenga | A. Isaacs | M. Beekman | L. Karssen | P. Slagboom | K. Estrada | A. Abdellaoui | V. Guryev | M. Vermaat | L. Francioli | Ruoyan Chen | Yuanping Du | S. Cao | A. Menelaou | C. Elbers | H. Byelas | Patrick Deelen | M. Dijkstra | V. Koval | A. Kanterakis | M. Kattenberg | B. Oostra | J. D. Dunnen | Eric-Wubbo Lameijer | N. Amin | S. Potluri | B. V. Schaik | MingKun Li | M. Kayser | P. Palamara | M. Platteel | P. D. Bakker | G. Ommen | C. Medina-Gomez | J. Setten | A. Craen | M. Sohail | L. Berg | Matthijs Moed | J. Bot | H. Suchiman | H. Mei | P. Slagboom | I. Nijman | M. Oven | P. Knijff | F. Dijk | E. M. Leeuwen | I. Renkens | A. Schönhuth | D. Vuzman | K. V. D. Velde | S. Pitts | P. Sundar | L. H. Berg | J. Laros | J. V. Setten | Yingrui Li | A. Uitterlinden | A. Hofman | A. Hofman | B. Oostra | D. Boomsma
[1] D. G. MacArthur,et al. Guidelines for investigating causality of sequence variants in human disease , 2014, Nature.
[2] Melissa J. Landrum,et al. RefSeq: an update on mammalian reference sequences , 2013, Nucleic Acids Res..
[3] Pieter B. T. Neerincx,et al. The Genome of the Netherlands: design, and project goals , 2013, European Journal of Human Genetics.
[4] Iman Hajirasouliha,et al. MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels , 2013, Bioinform..
[5] P. Sullivan,et al. Population structure, migration, and diversifying selection in the Netherlands , 2013, European Journal of Human Genetics.
[6] Emily H Turner,et al. Actionable, pathogenic incidental findings in 1,000 participants' exomes. , 2013, American journal of human genetics.
[7] D. Jordan,et al. Large Numbers of Genetic Variants Considered to be Pathogenic are Common in Asymptomatic Individuals , 2013, Human mutation.
[8] D. Goldstein,et al. Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes , 2013, PLoS genetics.
[9] Teri A. Manolio,et al. Bringing genome-wide association findings into clinical use , 2013, Nature Reviews Genetics.
[10] N. Patterson,et al. Estimating and interpreting FST: The impact of rare variants , 2013, Genome research.
[11] Michael Krawczak,et al. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease , 2013, Human Genetics.
[12] D. Goldstein,et al. Sequencing studies in human genetics: design and interpretation , 2013, Nature Reviews Genetics.
[13] Itsik Pe'er,et al. Inference of historical migration rates via haplotype sharing , 2013, Bioinform..
[14] Buhm Han,et al. Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens , 2013, PloS one.
[15] P. Visscher,et al. Interpreting the role of de novo protein-coding mutations in neuropsychiatric disease , 2013, Nature Genetics.
[16] Jan O. Korbel,et al. Phenotypic impact of genomic structural variation: insights from and for human disease , 2013, Nature Reviews Genetics.
[17] I. Adzhubei,et al. Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2 , 2013, Current protocols in human genetics.
[18] S. Gabriel,et al. Analysis of 6,515 exomes reveals a recent origin of most human protein-coding variants , 2012, Nature.
[19] Peter L. Ralph,et al. The Geography of Recent Genetic Ancestry across Europe , 2012, PLoS biology.
[20] Jonathan Marchini,et al. Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold , 2013, Bioinform..
[21] P. de Knijff,et al. Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history , 2013, Investigative Genetics.
[22] Lilia M. Iakoucheva,et al. Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation , 2012, Cell.
[23] I. Pe’er,et al. Length distributions of identity by descent reveal fine-scale demographic history. , 2012, American journal of human genetics.
[24] G. Abecasis,et al. Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. , 2012, American journal of human genetics.
[25] Li Jin,et al. MtDNA analysis of global populations support that major population expansions began before Neolithic Time , 2012, Scientific Reports.
[26] Kenny Q. Ye,et al. An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.
[27] Mark Gerstein,et al. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment , 2012, Bioinform..
[28] S. Steinberg,et al. Rate of de novo mutations and the importance of father’s age to disease risk , 2012, Nature.
[29] R. Handsaker,et al. Structural haplotypes and recent evolution of the human 17q21.31 region , 2012, Nature Genetics.
[30] J. Veltman,et al. De novo mutations in human genetic disease , 2012, Nature Reviews Genetics.
[31] Jacob A. Tennessen,et al. Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes , 2012, Science.
[32] Adam Kiezun,et al. Exome sequencing and the genetic basis of complex traits , 2012, Nature Genetics.
[33] L. Kiemeney,et al. How to kickstart a national biobanking infrastructure – experiences and prospects of BBMRI-NL , 2012 .
[34] Alexander Schliep,et al. CLEVER: clique-enumerating variant finder , 2012, Bioinform..
[35] Joseph K. Pickrell,et al. A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes , 2012, Science.
[36] O. Delaneau,et al. A linear complexity phasing method for thousands of genomes , 2011, Nature Methods.
[37] Greg Gibson,et al. Rare and common variants: twenty arguments , 2012, Nature Reviews Genetics.
[38] P. Visscher,et al. Five years of GWAS discovery. , 2012, American journal of human genetics.
[39] G. McVean,et al. Differential confounding of rare and common variants in spatially structured populations , 2011, Nature Genetics.
[40] Euan A Ashley,et al. Performance comparison of whole-genome sequencing platforms , 2011, Nature Biotechnology.
[41] J. Marchini,et al. Genotype Imputation with Thousands of Genomes , 2011, G3: Genes | Genomes | Genetics.
[42] M. Arfan Ikram,et al. The Rotterdam Study: 2012 objectives and design update , 2011, European journal of epidemiology.
[43] Gabor T. Marth,et al. Demographic history and rare allele sharing among human populations , 2011, Proceedings of the National Academy of Sciences.
[44] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[45] 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.
[46] Leonard H van den Berg,et al. Population based epidemiology of amyotrophic lateral sclerosis using capture–recapture methodology , 2011, Journal of Neurology, Neurosurgery & Psychiatry.
[47] M. DePristo,et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.
[48] Joshua M. Korn,et al. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale , 2011, Nature Genetics.
[49] B. Browning,et al. A fast, powerful method for detecting identity by descent. , 2011, American journal of human genetics.
[50] Emmanouil Collab. A map of human genome variation from population-scale sequencing , 2011, Nature.
[51] Harry Campbell,et al. Genomic Runs of Homozygosity Record Population History and Consanguinity , 2010, PloS one.
[52] Sharon R Grossman,et al. Integrating common and rare genetic variation in diverse human populations , 2010, Nature.
[53] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[54] Faraz Hach,et al. mrsFAST: a cache-oblivious algorithm for short-read mapping , 2010, Nature Methods.
[55] 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.
[56] L. Excoffier,et al. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows , 2010, Molecular ecology resources.
[57] M. King,et al. Genetic Heterogeneity in Human Disease , 2010, Cell.
[58] Huanming Yang,et al. De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.
[59] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[60] Robert B. Hartlage,et al. This PDF file includes: Materials and Methods , 2009 .
[61] Zhaoxia Yu,et al. Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies. , 2009, American journal of human genetics.
[62] Yutaka Suzuki,et al. Recount: expectation maximization based error correction tool for next generation sequencing data. , 2009, Genome informatics. International Conference on Genome Informatics.
[63] R. Wilson,et al. BreakDancer: An algorithm for high resolution mapping of genomic structural variation , 2009, Nature Methods.
[64] 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..
[65] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[66] P. Donnelly,et al. A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies , 2009, PLoS genetics.
[67] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[68] Manfred Kayser,et al. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation , 2009, Human mutation.
[69] P. Stenson,et al. The Human Gene Mutation Database: 2008 update , 2009, Genome Medicine.
[70] Alexander Gusev,et al. Whole population, genome-wide mapping of hidden relatedness. , 2009, Genome research.
[71] Max Kuhn,et al. Building Predictive Models in R Using the caret Package , 2008 .
[72] Amit R. Indap,et al. Genes mirror geography within Europe , 2008, Nature.
[73] Christian Gieger,et al. Correlation between Genetic and Geographic Structure in Europe , 2008, Current Biology.
[74] M. Stephens,et al. Interpreting principal component analyses of spatial population genetic variation , 2008, Nature Genetics.
[75] Ronald P. Stolk,et al. Universal risk factors for multifactorial diseases-LifeLines : a three-generation population-based study , 2008 .
[76] Ulrike von Luxburg,et al. A tutorial on spectral clustering , 2007, Stat. Comput..
[77] Zhaohui S. Qin,et al. A second generation human haplotype map of over 3.1 million SNPs , 2007, Nature.
[78] Manuel A. R. Ferreira,et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.
[79] Anita Brandstätter,et al. Generating population data for the EMPOP database - an overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example. , 2007, Forensic science international.
[80] Andy Liaw,et al. Classification and Regression by randomForest , 2007 .
[81] Ryan E. Mills,et al. An initial map of insertion and deletion (INDEL) variation in the human genome. , 2006, Genome research.
[82] D. Reich,et al. Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.
[83] K. Majamaa,et al. Analysis of mitochondrial DNA sequences in patients with isolated or combined oxidative phosphorylation system deficiency , 2006, Journal of Medical Genetics.
[84] Alfredo Coppa,et al. The Role of Selection in the Evolution of Human Mitochondrial Genomes , 2006, Genetics.
[85] S. Batzoglou,et al. Distribution and intensity of constraint in mammalian genomic sequence. , 2005, Genome research.
[86] Geoffrey B. Nilsen,et al. Whole-Genome Patterns of Common DNA Variation in Three Human Populations , 2005, Science.
[87] François Stricher,et al. SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs , 2004, Nucleic Acids Res..
[88] M. Olivier. A haplotype map of the human genome , 2003, Nature.
[89] D. Mackey,et al. Sequence analysis of the mitochondrial genomes from Dutch pedigrees with Leber hereditary optic neuropathy. , 2003, American journal of human genetics.
[90] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.
[91] J. V. Moran,et al. Initial sequencing and analysis of the human genome. , 2001, Nature.
[92] S. Pääbo,et al. Mitochondrial genome variation and the origin of modern humans , 2000, Nature.
[93] S Rozen,et al. Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.
[94] D. Turnbull,et al. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA , 1999, Nature Genetics.
[95] P. Green,et al. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.
[96] P Green,et al. Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.
[97] A. Torroni,et al. Classification of European mtDNAs from an analysis of three European populations. , 1996, Genetics.
[98] Nature Genetics , 1991, Nature.
[99] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[100] B S Weir,et al. Covariances of relatives stemming from a population undergoing mixed self and random mating. , 1984, Biometrics.
[101] F. Sanger,et al. Sequence and organization of the human mitochondrial genome , 1981, Nature.
[102] J. H. Ward. Hierarchical Grouping to Optimize an Objective Function , 1963 .