- Inference of population structure using multilocus genotype data
J K Pritchard
Department of Statistics, University of Oxford, United Kingdom
Genetics 155:945-59. 2000
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations...
- 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
..characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype...
- 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...
- A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
Bryan N Howie
Department of Statistics, University of Oxford, Oxford, UK
PLoS Genet 5:e1000529. 2009
b>Genotype imputation methods are now being widely used in the analysis of genome-wide association studies...
- Common SNPs explain a large proportion of the heritability for human height
Queensland Institute of Medical Research, Brisbane, Queensland, Australia
Nat Genet 42:565-9. 2010
..using a linear model analysis, and validated the estimation method with simulations based on the observed genotype data. We show that 45% of variance can be explained by considering all SNPs simultaneously...
- Biological, clinical and population relevance of 95 loci for blood lipids
Tanya M Teslovich
Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
Nature 466:707-13. 2010
..Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD...
- MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
Department of Genetics, Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, USA
Genet Epidemiol 34:816-34. 2010
..We have previously implemented a computationally efficient Markov Chain framework for genotype imputation and haplotyping in the freely available MaCH software package...
- The Drosophila melanogaster Genetic Reference Panel
Trudy F C Mackay
Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
Nature 482:173-8. 2012
..Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information...
- 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...
- Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection
Michael W Fried
University of North Carolina, Chapel Hill 27599, USA
N Engl J Med 347:975-82. 2002
..We compared the efficacy and safety of peginterferon alfa-2a plus ribavirin, interferon alfa-2b plus ribavirin, and peginterferon alfa-2a alone in the initial treatment of chronic hepatitis C...
- SNP detection for massively parallel whole-genome resequencing
Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China
Genome Res 19:1124-32. 2009
..Our analyses demonstrate that our method has a very low false call rate at any sequencing depth and excellent genome coverage at a high sequencing depth...
- A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
Robert J Elshire
Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
PLoS ONE 6:e19379. 2011
- A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase
Department of Statistics, University of Washington, Seattle, 98195 4322, USA
Am J Hum Genet 78:629-44. 2006
..We illustrate the utility of the model by applying it to dense single-nucleotide-polymorphism genotype data for the tasks of imputing missing genotypes and estimating haplotypic phase...
- Mapping copy number variation by population-scale genome sequencing
Ryan E Mills
Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA
Nature 470:59-65. 2011
..Our analytical framework and SV map serves as a resource for sequencing-based association studies...
- CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
Center for Computational Medicine and Biology, Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
Bioinformatics 23:1801-6. 2007
- Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
Genetics 164:1567-87. 2003
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci...
- Missing heritability and strategies for finding the underlying causes of complex disease
Evan E Eichler
Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
Nat Rev Genet 11:446-50. 2010
- Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
Jeffrey C Barrett
Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
Nat Genet 41:703-7. 2009
..01; overall P < 5 × 10(-8)) and 4 additional regions provided nominal evidence of replication (P < 0.05). The many new candidate genes suggested by these results include IL10, IL19, IL20, GLIS3, CD69 and IL27...
- Rapid SNP discovery and genetic mapping using sequenced RAD markers
Nathan A Baird
Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
PLoS ONE 3:e3376. 2008
..Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms...
- Common variants conferring risk of schizophrenia
deCODE Genetics, Sturlugata 8, IS 101 Reykjavik, Iceland
Nature 460:744-7. 2009
..2. Our findings implicating the MHC region are consistent with an immune component to schizophrenia risk, whereas the association with NRGN and TCF4 points to perturbation of pathways involved in brain development, memory and cognition...
- Genotype imputation
Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109 2029, USA
Annu Rev Genomics Hum Genet 10:387-406. 2009
b>Genotype imputation is now an essential tool in the analysis of genome-wide association scans. This technique allows geneticists to accurately evaluate the evidence for association at genetic markers that are not directly genotyped...
- Fast model-based estimation of ancestry in unrelated individuals
David H Alexander
Department of Biomathematics, University of California at Los Angeles, Los Angeles, California 90095, USA
Genome Res 19:1655-64. 2009
..Estimated ancestries, derived from multi-locus genotype data, can be used to perform a statistical correction for population stratification...
- Peginterferon-alpha2a and ribavirin combination therapy in chronic hepatitis C: a randomized study of treatment duration and ribavirin dose
Stephanos J Hadziyannis
Department of Medicine and Hepatology, Henry Dunant Hospital, Athens, Greece
Ann Intern Med 140:346-55. 2004
..Treatment with pegylated interferon (peginterferon) and ribavirin for 48 weeks is more effective than conventional interferon and ribavirin in patients with chronic hepatitis C...
- R/qtl: QTL mapping in experimental crosses
Karl W Broman
Department of Biostatistics, Johns Hopkins University, 615 N Wolfe St, Baltimore, MD 21205, USA
Bioinformatics 19:889-90. 2003
- Autism genome-wide copy number variation reveals ubiquitin and neuronal genes
Joseph T Glessner
Center for Applied Genomics, Children s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
Nature 459:569-73. 2009
- Fast and accurate genotype imputation in genome-wide association studies through pre-phasing
Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
Nat Genet 44:955-9. 2012
..sequencing efforts are producing large collections of haplotypes that can be used as reference panels for genotype imputation in genome-wide association studies (GWAS)...
- Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance
Institute for Genome Sciences and Policy, Center for Human Genome Variation, Duke University, Durham, North Carolina 27708, USA
Nature 461:399-401. 2009
..06 x 10(-25)) and African-Americans (P = 2.06 x 10(-3)). Because the genotype leading to better response is in substantially greater frequency in European than African populations, this ..
- 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
..Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications...
- Peginterferon alfa-2b plus ribavirin compared with interferon alfa-2b plus ribavirin for initial treatment of chronic hepatitis C: a randomised trial
M P Manns
Division of Gastroenterology and Hepatology, Medical School of Hannover, Hannover, Germany
Lancet 358:958-65. 2001
..In this randomised trial, peginterferon alfa-2b plus ribavirin was compared with interferon alfa-2b plus ribavirin...
- A simple and robust statistical test for detecting the presence of recombination
Trevor C Bruen
McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
Genetics 172:2665-81. 2006
..The results suggest that phi(w) is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances...
- Telaprevir with peginterferon and ribavirin for chronic HCV genotype 1 infection
John G McHutchison
Duke Clinical Research Institute and Duke University, Durham, NC 27715, USA
N Engl J Med 360:1827-38. 2009
..therapy for chronic hepatitis C virus (HCV) infection is effective in less than 50% of patients infected with HCV genotype 1...
- Rare variants create synthetic genome-wide associations
Samuel P Dickson
Institute for Genome Sciences and Policy, Center for Human Genome Variation, Duke University, Durham, North Carolina, USA
PLoS Biol 8:e1000294. 2010
..In conclusion, uncommon or rare genetic variants can easily create synthetic associations that are credited to common variants, and this possibility requires careful consideration in the interpretation and follow up of GWAS signals...
- Association of anxiety-related traits with a polymorphism in the serotonin transporter gene regulatory region
K P Lesch
Department of Psychiatry, University of Wurzburg, Fuchsleinstrasse 15, 97080 Wurzburg, Germany
Science 274:1527-31. 1996
- Genome-wide association analysis of metabolic traits in a birth cohort from a founder population
Department of Human Genetics and Los Angeles, Los Angeles, California 90095, USA
Nat Genet 41:35-46. 2009
..The association observed between low-density lipoprotein and an infrequent variant in AR suggests the potential of such a cohort for identifying associations with both common, low-impact and rarer, high-impact quantitative trait loci...
- 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
..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
- SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap
Andrew D Johnson
The Framingham Heart Study of the National Heart, Lung, and Blood Institute of the National Institutes of Health, USA
Bioinformatics 24:2938-9. 2008
- Genome-wide association study identifies five new breast cancer susceptibility loci
Section of Cancer Genetics, The Institute of Cancer Research, Sutton, Surrey, UK
Nat Genet 42:504-7. 2010
- The genetic structure and history of Africans and African Americans
Sarah A Tishkoff
Department of Biology, University of Maryland, College Park, MD 20742, USA
Science 324:1035-44. 2009
..This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies...
- Common regulatory variation impacts gene expression in a cell type-dependent manner
Antigone S Dimas
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1HH, Cambridge, UK
Science 325:1246-50. 2009
..These data suggest that the complete regulatory variant repertoire can only be uncovered in the context of cell-type specificity...
- Boceprevir for untreated chronic HCV genotype 1 infection
Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
N Engl J Med 364:1195-206. 2011
..The rate of sustained virologic response has been below 50% in cases of HCV genotype 1 infection...
- Reconstructing Indian population history
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 461:489-94. 2009
..We therefore predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically...
- 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...
- 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
..In addition, the results are relevant to the prospects of genetic ancestry testing; an individual's DNA can be used to infer their geographic origin with surprising accuracy-often to within a few hundred kilometres...
- Genotype imputation for genome-wide association studies
Department of Statistics, University of Oxford, Oxford, UK
Nat Rev Genet 11:499-511. 2010
..b>Genotype imputation has been used widely in the analysis of GWA studies to boost power, fine-map associations and ..
- Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
Nature 465:627-31. 2010
..Our study demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms...
- 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 unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals
Brian L Browning
Department of Statistics, University of Auckland, Auckland 1142, New Zealand
Am J Hum Genet 84:210-23. 2009
..particularly when imputing low-frequency variants, and that unphased reference panels can provide highly accurate genotype imputation...
- Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG)
Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
Arch Virol 156:1397-413. 2011
..This system assigns a specific genotype to each of the 11 genome segments of a particular RV strain according to established nucleotide percent cutoff ..
- An economic method for the fluorescent labeling of PCR fragments
Department of Neuropediatrics, Charite University Hospital, Augustenburger Platz 1, D 13353 Berlin, Germany
Nat Biotechnol 18:233-4. 2000
..A poor man's approach to genotyping for research and high-throughput diagnostics...
- Population analysis of large copy number variants and hotspots of human genetic disease
Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
Am J Hum Genet 84:148-61. 2009
..g., 3q29, 16p12, and 15q25.2) for further investigation. This study provides one of the first analyses of large, rare (0.1%-1%) CNVs in the general population, with insights relevant to future analyses of genetic disease...
- Sofosbuvir for hepatitis C genotype 2 or 3 in patients without treatment options
Ira M Jacobson
Weill Cornell Medical College, New York, NY 10021, USA
N Engl J Med 368:1867-77. 2013
Patients chronically infected with hepatitis C virus (HCV) genotype 2 or 3 for whom treatment with peginterferon is not an option, or who have not had a response to prior interferon treatment, currently have no approved treatment options...
- Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families
E H Corder
Department of Medicine, Joseph and Kathleen Bryan Alzheimer s Disease Research Center, Duke University Medical Center, Durham, NC 27710
Science 261:921-3. 1993
..Thus APOE-epsilon 4 gene dose is a major risk factor for late onset AD and, in these families, homozygosity for APOE-epsilon 4 was virtually sufficient to cause AD by age 80...
- The architecture of gene regulatory variation across multiple human tissues: the MuTHER study
Alexandra C Nica
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
PLoS Genet 7:e1002003. 2011
..Our results underline the need to account for the complexity of eQTL tissue-specificity in an effort to assess consequences of such variants for complex traits...
- The NCBI dbGaP database of genotypes and phenotypes
Matthew D Mailman
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892 6510, USA
Nat Genet 39:1181-6. 2007
..for Biotechnology Information has created the dbGaP public repository for individual-level phenotype, exposure, genotype and sequence data and the associations between them...
- Diversity of human copy number variation and multicopy genes
Peter H Sudmant
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
Science 330:641-6. 2010
..1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families...
- Genetic sensitivity to the environment: the case of the serotonin transporter gene and its implications for studying complex diseases and traits
Department of Psychology, and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
Am J Psychiatry 167:509-27. 2010
- Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis
INSERM U629, Institut Pasteur de Lille, 1, Rue du Prof Calmette, F 59019 Lille cedex, France
J Clin Microbiol 44:4498-510. 2006
..This 15-locus system is therefore proposed as the new standard for routine epidemiological discrimination of M. tuberculosis isolates and the 24-locus system as a high-resolution tool for phylogenetic studies...
- 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
..The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies...
- Genotype and SNP calling from next-generation sequencing data
Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
Nat Rev Genet 12:443-51. 2011
..Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data...
- A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25
Rayjean J Hung
International Agency for Research on Cancer IARC, Lyon 69008, France
Nature 452:633-7. 2008
..Our results provide compelling evidence of a locus at 15q25 predisposing to lung cancer, and reinforce interest in nicotinic acetylcholine receptors as potential disease candidates and chemopreventative targets...
- Bioinformatics challenges for genome-wide association studies
Jason H Moore
Department of Genetics, Department of Community and Family Medicine, Dartmouth Medical School, Lebanon, NH 03756, USA
Bioinformatics 26:445-55. 2010
..shift away from the biostatistical approach toward a more holistic approach that recognizes the complexity of the genotype-phenotype relationship that is characterized by significant heterogeneity and gene-gene and gene-environment ..
- Genome-wide genetic marker discovery and genotyping using next-generation sequencing
John W Davey
Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King s Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
Nat Rev Genet 12:499-510. 2011
- Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS
Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224, USA
Neuron 72:245-56. 2011
..Our findings indicate that repeat expansion in C9ORF72 is a major cause of both FTD and ALS...
- IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy
Storr Liver Unit, University of Sydney, Sydney, Australia
Nat Genet 41:1100-4. 2009
..sustained virological response (SVR) to PEG-IFN-alpha/RBV combination therapy in 293 Australian individuals with genotype 1 chronic hepatitis C, with validation in an independent replication cohort consisting of 555 individuals...
- Human papillomavirus genotype attribution in invasive cervical cancer: a retrospective cross-sectional worldwide study
Silvia de Sanjose
IDIBELL, Institut Català d Oncologia Catalan Institute of Oncology, L Hospitalet de Llobregat, Barcelona, Spain
Lancet Oncol 11:1048-56. 2010
..We aimed to provide novel and comprehensive data about the worldwide genotype distribution in patients with invasive cervical cancer.
- Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes
Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, United Kingdom
Hepatology 42:962-73. 2005
..Virus Database (Japan), euHCVdb (France), and Los Alamos (United States), met to re-examine the status of HCV genotype nomenclature, resolve conflicting genotype or subtype names among described variants of HCV, and draw up revised ..
- DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
Jordana T Bell
Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
Genome Biol 12:R10. 2011
..Here we measured methylation levels at 22,290 CpG dinucleotides in lymphoblastoid cell lines from 77 HapMap Yoruba individuals, for which genome-wide gene expression and genotype data were also available.
- Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism
Stephan J Sanders
Program on Neurogenetics, Yale University School of Medicine, 230 South Frontage Road, New Haven, CT 06520, USA
Neuron 70:863-85. 2011
..4 × 10(-7)). We estimate there are 130-234 ASD-related CNV regions in the human genome and present compelling evidence, based on cumulative data, for association of rare de novo events at 7q11.23, 15q11.2-13.1, 16p11.2, and Neurexin 1...
- Evaluation of next generation sequencing platforms for population targeted sequencing studies
Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
Genome Biol 10:R32. 2009
..To evaluate these platforms for this application, we analyzed human sequence generated by the Roche 454, Illumina GA, and the ABI SOLiD technologies for the same 260 kb in four individuals...
- CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
Genome Res 21:974-84. 2011
..Finally, by combining discovery and genotyping, we identified six potential de novo CNVs in two family trios...
- Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain
J Raphael Gibbs
Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS Genet 6:e1000952. 2010
..We believe these data, which we have made publicly available, will provide a critical step toward understanding the biological effects of genetic variation...
- Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment
Steven T Kalinowski
Department of Ecology, Montana State University, Bozeman, MT 59717, USA
Mol Ecol 16:1099-106. 2007
..0 and 2.0 of CERVUS to accommodate genotyping error miscalculate the probability of observing an erroneous genotype. Computer simulation and reanalysis of paternity in Rum red deer show that correcting this error increases ..
- Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines
Neuro Oncology Branch, National Cancer Institute, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
Cancer Cell 9:391-403. 2006
..from primary glioblastomas harbor extensive similarities to normal neural stem cells and recapitulate the genotype, gene expression patterns, and in vivo biology of human glioblastomas...
- A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD
Alan E Renton
Neuromuscular Diseases Research Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
Neuron 72:257-68. 2011
..The repeat expansion is also present in one-third of familial ALS cases of outbred European descent, making it the most common genetic cause of these fatal neurodegenerative diseases identified to date...
- Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: a genome-wide association study
University Clinic of Infectious Diseases, University Hospital Bern and University of Bern, Bern, Switzerland
Gastroenterology 138:1338-45, 1345.e1-7. 2010
..We performed a genome-wide association study to screen for host genetic determinants of HCV persistence and response to therapy...
- High-resolution genotyping by amplicon melting analysis using LCGreen
Carl T Wittwer
Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132, USA
Clin Chem 49:853-60. 2003
..Our aim was to develop a closed-tube system for genotyping and mutation scanning that did not require labeled oligonucleotides...
- A variant associated with nicotine dependence, lung cancer and peripheral arterial disease
Thorgeir E Thorgeirsson
deCODE Genetics, 101 Reykjavik, Iceland
Nature 452:638-42. 2008
..The findings provide a case study of a gene-environment interaction, highlighting the role of nicotine addiction in the pathology of other serious diseases...
- Estimation of effect size distribution from genome-wide association studies and implications for future discoveries
Ju Hyun Park
Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Rockville, Maryland, USA
Nat Genet 42:570-5. 2010
..However, for BPC cancers, which have modest familial aggregation, our analysis suggests that risk models based on common variants alone will have modest discriminatory power (63.5% area under curve), even with new discoveries...
- Invited review: reliability of genomic predictions for North American Holstein bulls
P M Vanraden
Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 2350, USA
J Dairy Sci 92:16-24. 2009
..Reliability increased more by doubling the number of bulls genotyped than the number of markers genotyped. Genomic prediction improves reliability by tracing the inheritance of genes even with small effects...
- Development and characterization of a high density SNP genotyping assay for cattle
Lakshmi K Matukumalli
Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia, United States of America
PLoS ONE 4:e5350. 2009
..The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle...
- Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach
Jesse A Poland
Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture Agricultural Research Service, Manhattan, Kansas, United States of America
PLoS ONE 7:e32253. 2012
..Finally, as a result of low per-sample costs, GBS will have broad application in genomics-assisted plant breeding programs...
- Telaprevir for retreatment of HCV infection
Johann Wolfgang Goethe University Medical Center, Frankfurt am Main, Germany
N Engl J Med 364:2417-28. 2011
Up to 60% of patients with hepatitis C virus (HCV) genotype 1 infection do not have a sustained virologic response to therapy with peginterferon alfa plus ribavirin.
- PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice
Institut de Genetique Humaine, UPR1142, CNRS, Montpellier, France
Science 327:836-40. 2010
..Our results provide a molecular basis for the distribution of meiotic recombination in mammals, in which the binding of PRDM9 to specific DNA sequences targets the initiation of recombination at specific locations in the genome...
- SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
Curtis P van Tassell
Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA
Nat Methods 5:247-52. 2008
..b>Genotype data for these 66 individuals validated 92% of 23,357 selected genome-wide SNPs, with a genotypic and sequence ..
- Common genetic variation and the control of HIV-1 in humans
Center for Human Genome Variation, Duke Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
PLoS Genet 5:e1000791. 2009
..This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians...
- Genome structural variation discovery and genotyping
Department of Genome Sciences, University of Washington School of Medicine, Foege S413C, 3720 15th Ave NE, Seattle, Washington, USA
Nat Rev Genet 12:363-76. 2011
..We argue that the long-term goal should be routine, cost-effective and high quality de novo assembly of human genomes to comprehensively assess all classes of structural variation...
- A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits
Yoon Shin Cho
Center for Genome Science, National Institute of Health, Seoul, Korea
Nat Genet 41:527-34. 2009
..2 x 10(-3), P = 1.4 x 10(-7) and P = 6.0 x 10(-4), respectively). This large-scale GWA analysis of well-characterized Korean population-based samples highlights previously unknown biological pathways...
- The relationship of DNA methylation with age, gender and genotype in twins and healthy controls
Marco P Boks
Rudolf Magnus Institute of Neuroscience, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
PLoS ONE 4:e6767. 2009
..The identification of CpG loci of which DNA methylation levels are under genetic control or are related to age or gender will facilitate further studies into the role of DNA methylation and disease...
- Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium
L A Farrer
Department of Neurology, Boston University School of Medicine, Mass 02118, USA
JAMA 278:1349-56. 1997
To examine more closely the association between apolipoprotein E (APOE) genotype and Alzheimer disease (AD) by age and sex in populations of various ethnic and racial denominations.
- 'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease?
George Davey Smith
University of Bristol, Department of Social Medicine, Canynge Hall, Whiteladies Road, Bristol BS8 2PR, UK
Int J Epidemiol 32:1-22. 2003
- Clinical risk factors, DNA variants, and the development of type 2 diabetes
Department of Clinical Sciences, Lund University, Malmo, Sweden
N Engl J Med 359:2220-32. 2008
..Type 2 diabetes mellitus is thought to develop from an interaction between environmental and genetic factors. We examined whether clinical or genetic factors or both could predict progression to diabetes in two prospective cohorts...
- Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology
Antonio M Ramos
Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands
PLoS ONE 4:e6524. 2009
- Epidemiology of hepatitis C virus infection in Pakistan
Nadeem Sajjad Raja
Department of Medical Microbiology, Southend University Hospital NHS Foundation Trust, Essex, United Kingdom
J Microbiol Immunol Infect 41:4-8. 2008
..Although at present a small proportion of those with chronic HCV infection develop liver failure or hepatocellular carcinoma, it is estimated that the incidence of these advanced disease complications will increase over the coming years...
- Development and implementation of high-throughput SNP genotyping in barley
Timothy J Close
Department of Botany and Plant Sciences, University of California UCR, Riverside, CA, 92521, USA
BMC Genomics 10:582. 2009
..maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear ..
- Boceprevir for previously treated chronic HCV genotype 1 infection
Bruce R Bacon
Saint Louis University School of Medicine, St Louis, Mo 63110 0250, USA
N Engl J Med 364:1207-17. 2011
In patients with chronic infection with hepatitis C virus (HCV) genotype 1 who do not have a sustained response to therapy with peginterferon-ribavirin, outcomes after retreatment are suboptimal...
- Dissection of genetically complex traits with extremely large pools of yeast segregants
Ian M Ehrenreich
Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA
Nature 464:1039-42. 2010
..Our method should have broad applications in yeast and can be extended to other organisms...
- GWAMA: software for genome-wide association meta-analysis
Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
BMC Bioinformatics 11:288. 2010
..Although statistical software analysis packages incorporate routines for meta-analysis, they are ill equipped to meet the challenges of the scale and complexity of data generated in genome-wide association studies...
- Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Nature 487:375-9. 2012
..An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome...
- An automated genotyping system for analysis of HIV-1 and other microbial sequences
Tulio de Oliveira
Evolution Group at the Zoology Department, University of Oxford, UK
Bioinformatics 21:3797-800. 2005
..Here, we describe the development of an automated genotyping system that can be easily applied to HIV-1 and other rapidly evolving viral pathogens...
- Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
Nat Commun 2:467. 2011
- 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...