- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
Genome Biol 10:R25. 2009
..For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory ..
- A map of human genome variation from population-scale sequencing
Richard M Durbin
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
Nature 467:1061-73. 2010
The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype...
- The human genome browser at UCSC
W James Kent
Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
Genome Res 12:996-1006. 2002
..The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users...
- PLINK: a tool set for whole-genome association and population-based linkage analyses
Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
Am J Hum Genet 81:559-75. 2007
..Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis...
- Comprehensive mapping of long-range interactions reveals folding principles of the human genome
Broad Institute of Harvard and Massachusetts Institute of Technology MIT, MA 02139, USA
Science 326:289-93. 2009
..We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase...
- Initial sequencing and analysis of the human genome
E S Lander
Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
Nature 409:860-921. 2001
The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution...
- Origins and functional impact of copy number variation in the human genome
Donald F Conrad
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
Nature 464:704-12. 2010
- High-resolution profiling of histone methylations in the human genome
Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
Cell 129:823-37. 2007
..Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology...
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Nature 447:799-816. 2007
..generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project...
- Accurate whole human genome sequencing using reversible terminator chemistry
David R Bentley
Illumina Cambridge Ltd Formerly Solexa Ltd, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK
Nature 456:53-9. 2008
..We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male ..
- Combinatorial patterns of histone acetylations and methylations in the human genome
Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA
Nat Genet 40:897-903. 2008
..Our data suggest that these histone modifications may act cooperatively to prepare chromatin for transcriptional activation...
- Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
Nathaniel D Heintzman
Ludwig Institute for Cancer Research, University of California San Diego UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653 USA
Nat Genet 39:311-8. 2007
..We determined the chromatin modification states in high resolution along 30 Mb of the human genome and found that active promoters are marked by trimethylation of Lys4 of histone H3 (H3K4), whereas enhancers ..
- Mapping short DNA sequencing reads and calling variants using mapping quality scores
The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
Genome Res 18:1851-8. 2008
..Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net...
- A census of human cancer genes
P Andrew Futreal
Cancer Genome Project, Human Genome Analysis Group and Pfam Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Cambs, CB10 1SA, UK
Nat Rev Cancer 4:177-83. 2004
- The structure of haplotype blocks in the human genome
Stacey B Gabriel
Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
Science 296:2225-9. 2002
..Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia...
- Patterns of somatic mutation in human cancer genomes
Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 446:153-8. 2007
Cancers arise owing to mutations in a subset of genes that confer growth advantage. The availability of the human genome sequence led us to propose that systematic resequencing of cancer genomes for mutations would lead to the discovery ..
- A new multipoint method for genome-wide association studies by imputation of genotypes
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Nat Genet 39:906-13. 2007
..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...
- The protein kinase complement of the human genome
SUGEN Inc, 230 East Grand Avenue, South San Francisco, CA 94080, USA
Science 298:1912-34. 2002
We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences...
- The consensus coding sequences of human breast and colorectal cancers
Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
Science 314:268-74. 2006
The elucidation of the human genome sequence has made it possible to identify genetic alterations in cancers in unprecedented detail...
- Principal components analysis corrects for stratification in genome-wide association studies
Alkes L Price
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nat Genet 38:904-9. 2006
..Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers...
- The genomic landscapes of human breast and colorectal cancers
Laura D Wood
Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
Science 318:1108-13. 2007
..These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy...
- Structural variation in the human genome and its role in disease
Department of Molecular, Baylor College of Medicine, Houston, Texas 77030, USA
Annu Rev Med 61:437-55. 2010
..Both recombination- and replication-based mechanisms for CNV formation have been described...
- The impact of retrotransposons on human genome evolution
CNRS UMR 6556 Ecologie, Evolution, Symbiose, Universite de Poitiers, 40 Avenue du Recteur Pineau, Poitiers, France
Nat Rev Genet 10:691-703. 2009
..over the past 80 million years of primate evolution and now account for approximately one-third of the human genome. In this Review, we focus on this major class of elements and discuss the many ways that they affect the human ..
- Genome-wide mapping of in vivo protein-DNA interactions
David S Johnson
Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305 5120, USA
Science 316:1497-502. 2007
..NRSF; also known as REST, for repressor element-1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [+/-50 base pairs (bp)], which facilitated our finding ..
- A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 103:1412-7. 2006
A striking feature of the human genome is the dearth of CpG dinucleotides (CpGs) interrupted occasionally by CpG islands (CGIs), regions with relatively high content of the dinucleotide...
- Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays
Complete Genomics, Inc, 2071 Stierlin Court, Mountain View, CA 94043, USA
Science 327:78-81. 2010
..The high accuracy, affordable cost of $4400 for sequencing consumables, and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies.
- The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
Department of Neuroscience, Biomedical Center, Box 593, 75 124 Uppsala, Sweden
Mol Pharmacol 63:1256-72. 2003
..Our novel approach of analyzing such large and diverse sequence sets may be useful for studies on GPCRs in other genomes and divergent protein families...
- High-resolution mapping and characterization of open chromatin across the genome
Alan P Boyle
Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
Cell 132:311-22. 2008
..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...
- Discovery and characterization of chromatin states for systematic annotation of the human genome
MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts, USA
Nat Biotechnol 28:817-25. 2010
A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease...
- Global variation in copy number in the human genome
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 444:444-54. 2006
..We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap ..
- Personalized copy number and segmental duplication maps using next-generation sequencing
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
Nat Genet 41:1061-7. 2009
..2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology...
- Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
Nat Genet 39:457-66. 2007
..Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation...
- Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes
MitoCheck Project Group, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
Nature 464:721-7. 2010
Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life...
- Targeted capture and massively parallel sequencing of 12 human exomes
Sarah B Ng
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Nature 461:272-6. 2009
..This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact...
- Core signaling pathways in human pancreatic cancers revealed by global genomic analyses
Sol Goldman Pancreatic Cancer Research Center, Ludwig Center and Howard Hughes Medical Institute at the Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
Science 321:1801-6. 2008
..Dysregulation of these core pathways and processes through mutation can explain the major features of pancreatic tumorigenesis...
- Genetics of gene expression and its effect on disease
deCODE Genetics, 101 Reykjavik, Iceland
Nature 452:423-8. 2008
..A core network module in humans and mice was identified that is enriched for genes involved in the inflammatory and immune response and has been found to be causally associated to obesity-related traits...
- The Ensembl genome database project
The Wellcome Trust Sanger Institute and European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
Nucleic Acids Res 30:38-41. 2002
..It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is ..
- Population genomics of human gene expression
Barbara E Stranger
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nat Genet 39:1217-24. 2007
..Our results strongly support an abundance of cis-regulatory variation in the human genome. Detection of trans effects is limited but suggests that regulatory variation may be the key primary effect ..
- The fundamental role of epigenetic events in cancer
Peter A Jones
USC Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, MS 8302L, Los Angeles, California 90089 9181, USA
Nat Rev Genet 3:415-28. 2002
..In this review, we discuss these epigenetic events and the molecular alterations that might cause them and/or underlie altered gene expression in cancer...
- PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Res 17:1665-74. 2007
..3%. Our results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density SNP genotyping...
- Relative impact of nucleotide and copy number variation on gene expression phenotypes
Barbara E Stranger
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Science 315:848-53. 2007
..Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans...
- A whole-genome association study of major determinants for host control of HIV-1
Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
Science 317:944-7. 2007
..These findings emphasize the importance of studying human genetic variation as a guide to combating infectious agents...
- A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
Science 321:956-60. 2008
..A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing...
- Worldwide human relationships inferred from genome-wide patterns of variation
Jun Z Li
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
Science 319:1100-4. 2008
..We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci...
- GENCODE: producing a reference annotation for ENCODE
Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK
Genome Biol 7:S4.1-9. 2006
..This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results...
- Assessing the evolutionary impact of amino acid mutations in the human genome
Adam R Boyko
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
PLoS Genet 4:e1000083. 2008
Quantifying the distribution of fitness effects among newly arising mutations in the human genome is key to resolving important debates in medical and evolutionary genetics...
- Annotating the human genome with Disease Ontology
John D Osborne
Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
BMC Genomics 10:S6. 2009
The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases.
- Strong association of de novo copy number mutations with autism
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
Science 316:445-9. 2007
..Affected genomic regions were highly heterogeneous and included mutations of single genes. These findings establish de novo germline mutation as a more significant risk factor for ASD than previously recognized...
- Widespread changes in protein synthesis induced by microRNAs
Max Delbruck Center for Molecular Medicine, Robert Rossle Str 10, D 13125 Berlin, Germany
Nature 455:58-63. 2008
..Finally, our data suggest that a miRNA can, by direct or indirect effects, tune protein synthesis from thousands of genes...
- How malaria has affected the human genome and what human genetics can teach us about malaria
Dominic P Kwiatkowski
Wellcome Trust Centre for Human Genetics and University Department of Paediatrics, Oxford, United Kingdom
Am J Hum Genet 77:171-92. 2005
..of children worldwide and the strongest known force for evolutionary selection in the recent history of the human genome. The past decade has seen growing evidence of ethnic differences in susceptibility to malaria and of the ..
- A map of recent positive selection in the human genome
Benjamin F Voight
Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
PLoS Biol 4:e72. 2006
..For this purpose we have developed a set of SNPs that can be used to tag the strongest approximately 250 signals of recent selection in each population...
- Recurring mutations found by sequencing an acute myeloid leukemia genome
Elaine R Mardis
Department of Genetics, Washington University, St Louis, MO 63110, USA
N Engl J Med 361:1058-66. 2009
..The full complement of DNA mutations that are responsible for the pathogenesis of acute myeloid leukemia (AML) is not yet known...
- Human l1 retrotransposition is associated with genetic instability in vivo
David E Symer
Department of Molecular Biology and Genetics, John Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Cell 110:327-38. 2002
..In a striking number of integrants, short identical sequences were shared between the donor and the target site's 3' end, suggesting a mechanistic model that helps explain the structure of L1 insertions...
- Genome-wide detection and characterization of positive selection in human populations
Pardis C Sabeti
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
Nature 449:913-8. 2007
..of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (..
- The transcriptional landscape of the mammalian genome
Science 309:1559-63. 2005
..The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development...
- VISTA: computational tools for comparative genomics
Kelly A Frazer
Perlegen Sciences, Inc, 2021 Stierlin Court, Mountain View, CA 94043, USA
Nucleic Acids Res 32:W273-9. 2004
..We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein...
- Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
Peter J Campbell
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
Nat Genet 40:722-9. 2008
..By investigating read pairs that did not align correctly with respect to each other on the reference human genome, we characterized 306 germline structural variants and 103 somatic rearrangements to the base-pair level of ..
- Newly identified loci that influence lipid concentrations and risk of coronary artery disease
Cristen J Willer
Center for Statistical Genetics, Department of Biostatistics, University of Michigan, 1420 Washington Heights, Ann Arbor, Michigan 48109, USA
Nat Genet 40:161-9. 2008
..Notably, the 11 independent variants associated with increased LDL cholesterol concentrations in our study also showed increased frequency in a sample of coronary artery disease cases versus controls...
- MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Ave, mail code NE50, Cleveland, OH 44195, USA
Nucleic Acids Res 38:391-9. 2010
..This technique is highly specific and sensitive and can be applied to any biological settings to identify differentially methylated regions at the genomic scale...
- A human genome structural variation sequencing resource reveals insights into mutational mechanisms
Jeffrey M Kidd
Department of Genome Sciences, University of Washington School of Medicine, Seattle, 98195, USA
Cell 143:837-47. 2010
Understanding the prevailing mutational mechanisms responsible for human genome structural variation requires uniformity in the discovery of allelic variants and precision in terms of breakpoint delineation...
- Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease
Jeffrey C Barrett
Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Nat Genet 40:955-62. 2008
..The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development...
- Initial sequencing and comparative analysis of the mouse genome
Robert H Waterston
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 420:520-62. 2002
The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research...
- Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits
Unità Operativa Geriatria, Istituto per la Patologia Endocrina e Metabolica, Rome, Italy
PLoS Genet 3:e115. 2007
..These changes could have a significant impact on the risk of obesity-related morbidity in the general population...
- The sequence of the human genome
J C Venter
Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
Science 291:1304-51. 2001
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14...
- High-resolution mapping of expression-QTLs yields insight into human gene regulation
Jean Baptiste Veyrieras
Department of Human Genetics, The University of Chicago, Chicago, IL, USA
PLoS Genet 4:e1000214. 2008
..Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation...
- Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
Joshua M Korn
Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
Nat Genet 40:1253-60. 2008
..The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype...
- Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
Sohrab P Shah
Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada
Nature 461:809-13. 2009
..Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression...
- Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers
George Adrian Calin
Department of Microbiology and Immunology, Division of Clinical Pharmacology, Biostatistics Section, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
Proc Natl Acad Sci U S A 101:2999-3004. 2004
..These data provide a catalog of miR genes that may have roles in cancer and argue that the full complement of miRs in a genome may be extensively involved in cancers...
- Signals of recent positive selection in a worldwide sample of human populations
Joseph K Pickrell
Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
Genome Res 19:826-37. 2009
..we present an analysis of recent selection in a global sample of 53 populations, using genotype data from the Human Genome Diversity-CEPH Panel...
- Bayesian inference of epistatic interactions in case-control studies
Department of Statistics, The Pennsylvania State University, Thomas Building 422A, University Park, Pennsylvania 16802, USA
Nat Genet 39:1167-73. 2007
Epistatic interactions among multiple genetic variants in the human genome may be important in determining individual susceptibility to common diseases...
- Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
Alayne L Brunner
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
Genome Res 19:1044-56. 2009
..Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation...
- The impact of recombination on nucleotide substitutions in the human genome
Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, Universite Lyon 1, CNRS, UMR 5558, Villeurbanne, France
PLoS Genet 4:e1000071. 2008
..We show that the predictions of this model fit very well with the observed substitution patterns in the human genome. This model notably explains the positive correlation between substitution rate and recombination rate...
- An evolutionary view of human recombination
Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Rev Genet 8:23-34. 2007
- Mapping the genetic architecture of gene expression in human liver
Eric E Schadt
Rosetta Inpharmatics, Seattle, Washington, United States of America
PLoS Biol 6:e107. 2008
..We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process...
- A small-cell lung cancer genome with complex signatures of tobacco exposure
Erin D Pleasance
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
Nature 463:184-90. 2010
..These findings illustrate the potential for next-generation sequencing to provide unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with cancer...
- HIV-1 integration in the human genome favors active genes and local hotspots
Astrid R W Schroder
Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
Cell 110:521-9. 2002
..Here we describe mapping of 524 sites of HIV cDNA integration on the human genome sequence. Genes were found to be strongly favored as integration acceptor sites...
- Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis
Yurii S Aulchenko
Department of Epidemiology and Biostatistics, Erasmus MC, 3000 CA Rotterdam, The Netherlands
Genetics 177:577-85. 2007
..However, there is little or no difference in empirical power of MG and the proposed method. In any scenario, GRAMMAR is much faster than MG and enables rapid analysis of hundreds of thousands of markers...
- Discovery and annotation of functional chromatin signatures in the human genome
Bioinformatics Program, University of California at San Diego, La Jolla, California, United States of America
PLoS Comput Biol 5:e1000566. 2009
..To identify novel chromatin signatures in the human genome, we apply a de novo pattern-finding algorithm to genome-wide maps of histone modifications...
- Mobile interspersed repeats are major structural variants in the human genome
Cheng Ran Lisa Huang
Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
Cell 141:1171-82. 2010
Characterizing structural variants in the human genome is of great importance, but a genome wide analysis to detect interspersed repeats has not been done...
- Towards a comprehensive structural variation map of an individual human genome
Andy W Pang
Department of Molecular Genetics, University of Toronto, 1 King s College Circle, Toronto, Ontario M5S 1A8, Canada
Genome Biol 11:R52. 2010
..It is still unclear to what extent a typical genome differs from the reference assembly, and the analysis of the genomes sequenced to date have shown varying results for copy number variation (CNV) and inversions...
- Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans
Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
Nat Genet 40:189-97. 2008
..Understanding the molecular, cellular and clinical consequences of the newly identified loci may inform therapy and clinical care...
- ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome
Bioinformatics Program, University of California San Diego, La Jolla, California, United States of America
PLoS Comput Biol 4:e1000201. 2008
..Applying this algorithm to nine chromatin marks across a 1% sampling of the human genome in HeLa cells, we recover eight clusters of distinct chromatin signatures, five of which correspond to known ..
- Integrating multiple evidence sources to predict transcription factor binding in the human genome
Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
Genome Res 20:526-36. 2010
..When combined with motif information our method outperforms previous methods for predicting locations of true binding...
- A fine-scale map of recombination rates and hotspots across the human genome
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Science 310:321-4. 2005
..We present a high-resolution genetic map of the human genome, based on statistical analyses of genetic variation data, and identify more than 25,000 recombination hotspots, ..
- High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications
Tamim H Shaikh
Division of Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
Genome Res 19:1682-90. 2009
..Together, this analysis and annotation provides a useful resource to assist with the assessment of CNVs in the contexts of human variation, disease susceptibility, and clinical molecular diagnostics...
- Single-molecule sequencing of an individual human genome
Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, California, USA
Nat Biotechnol 27:847-50. 2009
..Here we report the use of single-molecule methods to sequence an individual human genome. We aligned billions of 24- to 70-bp reads (32 bp average) to approximately 90% of the National Center for ..
- Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells
Genome Center of Wisconsin, University of Wisconsin Madison, 425 Henry Mall, Madison, WI 53706 1580, USA
Cell Stem Cell 1:299-312. 2007
..Our results demonstrate that H3K27me3 modifications change during early differentiation, both relieving existing repressive domains and imparting new ones, and that colocalization with H3K4me3 is not restricted to pluripotent cells...
- Genes mirror geography within Europe
Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095, USA
Nature 456:98-101. 2008
..variation in a sample of 3,000 European individuals genotyped at over half a million variable DNA sites in the human genome. Despite low average levels of genetic differentiation among Europeans, we find a close correspondence between ..
- QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data
Genomics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, UK
Nucleic Acids Res 35:2013-25. 2007
Array-based technologies have been used to detect chromosomal copy number changes (aneuploidies) in the human genome. Recent studies identified numerous copy number variants (CNV) and some are common polymorphisms that may contribute to ..
- MAX-rank: a simple and robust genome-wide scan for case-control association studies
Biostatistics Branch, National Cancer Institute, Bethesda, MD 20892, USA
Hum Genet 123:617-23. 2008
..Thus, we recommend to use MAX-rank for genome-wide scans. After the top-ranked SNPs are identified, their P-values based on MAX can be calculated and compared with the significance level...
- Evidence for large inversion polymorphisms in the human genome from HapMap data
Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093 0004, USA
Genome Res 17:219-30. 2007
Knowledge about structural variation in the human genome has grown tremendously in the past few years. However, inversions represent a class of structural variation that remains difficult to detect...
- Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes
Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, OX3 7LJ, UK
Science 316:1336-41. 2007
..The regions identified underscore the importance of pathways influencing pancreatic beta cell development and function in the etiology of type 2 diabetes...
- Druggability of human disease genes
Meena Kishore Sakharkar
Nanyang Centre for Supercomputing and Visualization, School of Mechanical and Aerospace Engineering MAE, Nanyang Technological University, Singapore
Int J Biochem Cell Biol 39:1156-64. 2007
..to provide an accurate description of gene functions to a set of 1737 highly curated disease genes in the human genome. This analysis is the first attempt on in silico identification of druggable domains within disease genes...
- Are linkage analysis and the collection of family data dead? Prospects for family studies in the age of genome-wide association
Hum Hered 64:91-6. 2007
- A genomewide admixture mapping panel for Hispanic/Latino populations
Department of Anthropology, The Pennsylvania State University, University Park, PA 16801, USA
Am J Hum Genet 80:1171-8. 2007
..This genomewide AM panel will make it possible to apply AM approaches in many admixed populations throughout the Americas...
- The complete genome of an individual by massively parallel DNA sequencing
David A Wheeler
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
Nature 452:872-6. 2008
..However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete ..
- Genome-wide association analysis in sarcoidosis and Crohn's disease unravels a common susceptibility locus on 10p12.2
Institute for Clinical Molecular Biology, Christian Albrechts University, Kiel, Germany
Gastroenterology 135:1207-15. 2008
..Crohn's disease (CD) and sarcoidosis (SA) are chronic inflammatory barrier diseases that share several clinical and immunological features, including the occurrence of granulomas...
- Expression of Kruppel-like factor 5 gene in human brain and association of the gene with the susceptibility to schizophrenia
Division of Psychiatry and Neurology, Department of Environmental Health and Safety, Faculty of Medical Sciences, Kobe University Graduate School of Medicine, Kobe, Japan
Schizophr Res 100:291-301. 2008
..These findings suggest that the KLF5 gene is a novel schizophrenia-susceptibility gene, and that the expression of the gene is involved in the pathophysiology of schizophrenia via glutamatergic neurotransmission...
- Selection of genes and single nucleotide polymorphisms for fine mapping starting from a broad linkage region
Research Center for Exercise and Health, Department of Biomedical Kinesiology, Faculty of Kinesiology and Rehabilitation Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
Twin Res Hum Genet 10:871-85. 2007
..This resulted in the selection of 331 polymorphisms located in 112 different candidate genes out of an initial set of 23,300 SNPs...
- A fast boosting-based screening method for large-scale association study in complex traits with genetic heterogeneity
Lu Yong Wang
Integrated Data Syst Dept, Siemens Corp Res Inc, Princeton, NJ 08540, USA
Conf Proc IEEE Eng Med Biol Soc 1:5771-4. 2006
..It provides a relatively fast and fairly good tool for screening and limiting the candidate SNPs for further more complex computational modeling task...