Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

[1]  M. P. Concas,et al.  Height-reducing variants and selection for short stature in Sardinia , 2015, Nature Genetics.

[2]  Carlo Sidore,et al.  Rare variant genotype imputation with thousands of study-specific whole-genome sequences: implications for cost-effective study designs , 2014, European Journal of Human Genetics.

[3]  G. Abecasis,et al.  An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data , 2015, Genome research.

[4]  T. Spector,et al.  GENOME-WIDE ASSOCIATION ANALYSES BASED ON WHOLE-GENOME SEQUENCING IN SARDINIA PROVIDE INSIGHTS INTO REGULATION OF HEMOGLOBIN LEVELS , 2015, Nature Genetics.

[5]  Jie Huang,et al.  Whole-genome sequence-based analysis of thyroid function , 2015, Nature communications.

[6]  Pierre Fontanillas,et al.  Association of exome sequences with plasma C-reactive protein levels in >9000 participants. , 2015, Human molecular genetics.

[7]  J. Al-Aama,et al.  A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes , 2014, Nature.

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

[9]  E. Zeggini,et al.  Estimating Genome-Wide Significance for Whole-Genome Sequencing Studies , 2014, Genetic epidemiology.

[10]  J. Shendure,et al.  A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.

[11]  M. Daly,et al.  Searching for missing heritability: Designing rare variant association studies , 2014, Proceedings of the National Academy of Sciences.

[12]  Gil McVean,et al.  Demography and the Age of Rare Variants , 2014, PLoS genetics.

[13]  Xiaowei Zhan,et al.  QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data , 2013, BioMed research international.

[14]  Tanya M. Teslovich,et al.  Discovery and refinement of loci associated with lipid levels , 2013, Nature Genetics.

[15]  Tanya M. Teslovich,et al.  Common variants associated with plasma triglycerides and risk for coronary artery disease , 2013, Nature Genetics.

[16]  Wieslawa I. Mentzen,et al.  Genetic Variants Regulating Immune Cell Levels in Health and Disease , 2013, Cell.

[17]  Miles Parkes,et al.  Genetic insights into common pathways and complex relationships among immune-mediated diseases , 2013, Nature Reviews Genetics.

[18]  S. Tofanelli,et al.  Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny , 2013, Science.

[19]  N. Patterson,et al.  Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits , 2013, PLoS genetics.

[20]  Alireza Moayyeri,et al.  COHORT PROFILE Cohort Profile : TwinsUK and Healthy Ageing Twin Study , 2013 .

[21]  A. Kijlstra,et al.  Genetic Variant on PDGFRL Associated with Behçet Disease in Chinese Han Populations , 2013, Human mutation.

[22]  X. Estivill,et al.  Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity , 2012, European Journal of Human Genetics.

[23]  P. Visscher,et al.  Genome-wide complex trait analysis (GCTA): methods, data analyses, and interpretations. , 2013, Methods in molecular biology.

[24]  Wei Chen,et al.  Genotype calling and haplotyping in parent-offspring trios , 2013, Genome research.

[25]  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.

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

[27]  Patrick F. Sullivan,et al.  zCall: a rare variant caller for array-based genotyping: Genetics and population analysis , 2012, Bioinform..

[28]  G. Abecasis,et al.  Exome sequencing and complex disease: practical aspects of rare variant association studies , 2012, Human molecular genetics.

[29]  Tanya M. Teslovich,et al.  The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits , 2012, PLoS genetics.

[30]  J. Marchini,et al.  Fast and accurate genotype imputation in genome-wide association studies through pre-phasing , 2012, Nature Genetics.

[31]  Claudio J. Verzilli,et al.  An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People , 2012, Science.

[32]  Paul Scheet,et al.  A Genome-Wide Association Scan on the Levels of Markers of Inflammation in Sardinians Reveals Associations That Underpin Its Complex Regulation , 2012, PLoS genetics.

[33]  Christopher G Chute,et al.  Complement receptor 1 gene variants are associated with erythrocyte sedimentation rate. , 2011, American journal of human genetics.

[34]  Gabor T. Marth,et al.  Demographic history and rare allele sharing among human populations , 2011, Proceedings of the National Academy of Sciences.

[35]  Gonçalo R. Abecasis,et al.  Fine Mapping of Five Loci Associated with Low-Density Lipoprotein Cholesterol Detects Variants That Double the Explained Heritability , 2011, PLoS genetics.

[36]  G. Abecasis,et al.  Low-coverage sequencing: implications for design of complex trait association studies. , 2011, Genome research.

[37]  F. Wright,et al.  CONVERGENCE AND PREDICTION OF PRINCIPAL COMPONENT SCORES IN HIGH-DIMENSIONAL SETTINGS. , 2012, Annals of statistics.

[38]  G. Abecasis,et al.  MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes , 2010, Genetic epidemiology.

[39]  Michael Boehnke,et al.  LocusZoom: regional visualization of genome-wide association scan results , 2010, Bioinform..

[40]  Yun Li,et al.  METAL: fast and efficient meta-analysis of genomewide association scans , 2010, Bioinform..

[41]  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 .

[42]  Gianmauro Cuccuru,et al.  Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis , 2010, Nature Genetics.

[43]  Raffaella Origa,et al.  BETA THALASSEMIA , 2018, The Professional Medical Journal.

[44]  Margaret A. Pericak-Vance,et al.  Genetic variants near TIMP3 and high-density lipoprotein–associated loci influence susceptibility to age-related macular degeneration , 2010, Proceedings of the National Academy of Sciences.

[45]  H. Kang,et al.  Variance component model to account for sample structure in genome-wide association studies , 2010, Nature Genetics.

[46]  N. Warrington,et al.  Apolipoprotein E genotype is associated with serum C-reactive protein but not abdominal aortic aneurysm. , 2010, Atherosclerosis.

[47]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[48]  Shamil R Sunyaev,et al.  Pooled association tests for rare variants in exon-resequencing studies. , 2010, American journal of human genetics.

[49]  Enrico Petretto,et al.  Heritability and Demographic Analyses in the Large Isolated Population of Val Borbera Suggest Advantages in Mapping Complex Traits Genes , 2009, PloS one.

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

[51]  Chenwei Wang,et al.  Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma , 2009, Nature Genetics.

[52]  J. Stamatoyannopoulos,et al.  Power of deep, all-exon resequencing for discovery of human trait genes , 2009, Proceedings of the National Academy of Sciences.

[53]  E. Stone,et al.  Co-Regulated Transcriptional Networks Contribute to Natural Genetic Contribute Variation in Drosophila Sleep , 2009, Nature Genetics.

[54]  F. Cucca,et al.  Variation within the CLEC16A gene shows consistent disease association with both multiple sclerosis and type 1 diabetes in Sardinia , 2009, Genes and Immunity.

[55]  G. Abecasis,et al.  Genotype imputation. , 2009, Annual review of genomics and human genetics.

[56]  Christian Gieger,et al.  Six new loci associated with body mass index highlight a neuronal influence on body weight regulation , 2009, Nature Genetics.

[57]  Amit R. Indap,et al.  Genes mirror geography within Europe , 2008, Nature.

[58]  John Novembre,et al.  The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. , 2008, American journal of human genetics.

[59]  S. Leal,et al.  Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. , 2008, American journal of human genetics.

[60]  John D. Storey,et al.  Mapping the Genetic Architecture of Gene Expression in Human Liver , 2008, PLoS biology.

[61]  M. McCarthy,et al.  Genome-wide association studies for complex traits: consensus, uncertainty and challenges , 2008, Nature Reviews Genetics.

[62]  M. West,et al.  An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer , 2008, BMC Genomics.

[63]  David Reich,et al.  Discerning the Ancestry of European Americans in Genetic Association Studies , 2007, PLoS genetics.

[64]  G. Abecasis,et al.  Family-based association tests for genomewide association scans. , 2007, American journal of human genetics.

[65]  R. Collins,et al.  Cholesterol fractions and apolipoproteins as risk factors for heart disease mortality in older men. , 2007, Archives of internal medicine.

[66]  Alastair Forbes,et al.  Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility , 2007, Nature Genetics.

[67]  Joshua T. Burdick,et al.  In silico method for inferring genotypes in pedigrees , 2006, Nature Genetics.

[68]  G. Abecasis,et al.  Heritability of Cardiovascular and Personality Traits in 6,148 Sardinians , 2006, PLoS genetics.

[69]  Jing Ma,et al.  Inflammatory markers and the risk of coronary heart disease in men and women. , 2004, The New England journal of medicine.

[70]  L L Cavalli-Sforza,et al.  Peopling of three Mediterranean islands (Corsica, Sardinia, and Sicily) inferred by Y-chromosome biallelic variability. , 2003, American journal of physical anthropology.

[71]  Jingfei Huang,et al.  Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation , 2002, Journal of molecular modeling.

[72]  G. Abecasis,et al.  Merlin—rapid analysis of dense genetic maps using sparse gene flow trees , 2002, Nature Genetics.

[73]  W. März,et al.  Rationale and design of the LURIC study--a resource for functional genomics, pharmacogenomics and long-term prognosis of cardiovascular disease. , 2001, Pharmacogenomics.

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

[75]  J. Todd,et al.  Major factors influencing linkage disequilibrium by analysis of different chromosome regions in distinct populations: demography, chromosome recombination frequency and selection. , 2000, Human molecular genetics.

[76]  Kenneth Lange,et al.  Use of population isolates for mapping complex traits , 2000, Nature Reviews Genetics.

[77]  M. Reid.  Arg89Cys substitution results in very low membrane expression of the Duffy antigen/receptor for chemokines in Fyx individuals , 1999 .

[78]  P. Gane,et al.  Arg89Cys substitution results in very low membrane expression of the Duffy antigen/receptor for chemokines in Fy(x) individuals. , 1998, Blood.

[79]  M. Maioli,et al.  Plasma lipoprotein composition, apolipoprotein(a) concentration and isoforms in beta-thalassemia. , 1997, Atherosclerosis.

[80]  S. Pettinato,et al.  Plasma lipids in beta-thalassemia minor. , 1989, Atherosclerosis.