Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes

[1]  K. Suhre,et al.  Whole genome sequencing in the Middle Eastern Qatari population identifies genetic associations with 45 clinically relevant traits , 2021, Nature communications.

[2]  M. Falchi,et al.  Ethnic-specific association of amylase gene copy number with adiposity traits in a large Middle Eastern biobank , 2021, NPJ genomic medicine.

[3]  T. Gojobori,et al.  Population structure of indigenous inhabitants of Arabia. , 2021, PLoS genetics.

[4]  Arslan A. Zaidi,et al.  Demographic history mediates the effect of stratification on polygenic scores , 2020, eLife.

[5]  D. Reich,et al.  The Genomic History of the Bronze Age Southern Levant , 2020, Cell.

[6]  D. Reich,et al.  The Spread of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean , 2020, Nature Ecology & Evolution.

[7]  Kamal M. Osman,et al.  Point of Care Exome Sequencing Reveals Allelic and Phenotypic Heterogeneity Underlying Mendelian disease in Qatar. , 2019, Human molecular genetics.

[8]  C. Bustamante,et al.  Ancient DNA reconstructs the genetic legacies of pre-contact Puerto Rico communities. , 2019, Molecular biology and evolution.

[9]  C. Bustamante,et al.  Ancient DNA reconstructs the genetic legacies of pre-contact Puerto Rico communities , 2019, bioRxiv.

[10]  N. Afifi,et al.  Qatar Biobank Cohort Study: Study Design and First Results. , 2019, American journal of epidemiology.

[11]  J. Tuomilehto,et al.  Assessment of coding region variants in Kuwaiti population: implications for medical genetics and population genomics , 2018, Scientific Reports.

[12]  Brian L Browning,et al.  Genotype Imputation from Large Reference Panels. , 2018, Annual review of genomics and human genetics.

[13]  Gabriel Renaud,et al.  glactools: a command-line toolset for the management of genotype likelihoods and allele counts , 2017, bioRxiv.

[14]  Laura T. Buck,et al.  Homo sapiens in Arabia by 85,000 years ago , 2018, Nature Ecology & Evolution.

[15]  Peter K. Joshi,et al.  Runs of homozygosity: windows into population history and trait architecture , 2018, Nature Reviews Genetics.

[16]  Daniel G. MacArthur,et al.  Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity , 2017, Nature.

[17]  Mohammad Afzal,et al.  Genetics of consanguinity and inbreeding in health and disease , 2017, Annals of human biology.

[18]  Yun S. Song,et al.  Robust and scalable inference of population history from hundreds of unphased whole genomes , 2016, Nature Genetics.

[19]  G. D. Poznik.  Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men , 2016, bioRxiv.

[20]  G. Hellenthal,et al.  Recent Historical Migrations Have Shaped the Gene Pool of Arabs and Berbers in North Africa , 2016, Molecular biology and evolution.

[21]  Zachary A. Szpiech,et al.  A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome , 2016, Nature Communications.

[22]  Alan M. Kwong,et al.  Next-generation genotype imputation service and methods , 2016, Nature Genetics.

[23]  Luca Scrucca,et al.  mclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models , 2016, R J..

[24]  Swapan Mallick,et al.  Genomic insights into the origin of farming in the ancient Near East , 2016, Nature.

[25]  Anason S. Halees,et al.  Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery , 2016, Nature Genetics.

[26]  Yun S. Song,et al.  The Simons Genome Diversity Project: 300 genomes from 142 diverse populations , 2016, Nature.

[27]  Shane A. McCarthy,et al.  Reference-based phasing using the Haplotype Reference Consortium panel , 2016, Nature Genetics.

[28]  Mahmoud Zirie,et al.  The Qatar genome: a population-specific tool for precision medicine in the Middle East , 2016, Human Genome Variation.

[29]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, bioRxiv.

[30]  A. Clark,et al.  Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations , 2016, Genome research.

[31]  Yali Xue,et al.  BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data , 2016, Bioinform..

[32]  Mannis van Oven,et al.  PhyloTree Build 17: Growing the human mitochondrial DNA tree , 2015 .

[33]  A. Eriksson,et al.  Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa , 2015, Science.

[34]  J. Mezey,et al.  Copy number variations in the genome of the Qatari population , 2015, BMC Genomics.

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

[36]  Richard P. Jennings,et al.  The greening of Arabia: Multiple opportunities for human occupation of the Arabian Peninsula during the Late Pleistocene inferred from an ensemble of climate model simulations , 2015 .

[37]  Tom R. Gaunt,et al.  Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel , 2015, Nature Communications.

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

[39]  Bjarni V. Halldórsson,et al.  Large-scale whole-genome sequencing of the Icelandic population , 2015, Nature Genetics.

[40]  Carson C Chow,et al.  Second-generation PLINK: rising to the challenge of larger and richer datasets , 2014, GigaScience.

[41]  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.

[42]  K. Hemminki,et al.  Consanguinity and genetic diseases in North Africa and immigrants to Europe. , 2014, European journal of public health.

[43]  Olivier Delaneau,et al.  Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel , 2014, Nature Communications.

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

[45]  D. Falush,et al.  A Genetic Atlas of Human Admixture History , 2014, Science.

[46]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[47]  J. Mezey,et al.  Exome Sequencing Identifies Potential Risk Variants for Mendelian Disorders at High Prevalence in Qatar , 2014, Human mutation.

[48]  Bonnie Berger,et al.  Ancient human genomes suggest three ancestral populations for present-day Europeans , 2013, Nature.

[49]  Samantha Lycett,et al.  Automated analysis of phylogenetic clusters , 2013, BMC Bioinformatics.

[50]  G. Abecasis,et al.  Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females , 2013, Science.

[51]  Zachary A. Szpiech,et al.  Long runs of homozygosity are enriched for deleterious variation. , 2013, American journal of human genetics.

[52]  Christopher R. Gignoux,et al.  Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data , 2013, PLoS genetics.

[53]  Jake K. Byrnes,et al.  Reconstructing the Population Genetic History of the Caribbean , 2013, PLoS genetics.

[54]  Elizabeth Matisoo-Smith,et al.  Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations , 2013, PloS one.

[55]  Swapan Mallick,et al.  Ancient Admixture in Human History , 2012, Genetics.

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

[57]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[58]  Richard M Myers,et al.  Genomic patterns of homozygosity in worldwide human populations. , 2012, American journal of human genetics.

[59]  Joseph K. Pickrell,et al.  Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data , 2012, PLoS genetics.

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

[61]  Christopher R. Gignoux,et al.  History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico , 2011, PloS one.

[62]  Günther Specht,et al.  HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups , 2011, Human mutation.

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

[64]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[65]  A. Clark,et al.  Population genetic structure of the people of Qatar. , 2010, American journal of human genetics.

[66]  Laurent Gil,et al.  Ensembl variation resources , 2010, BMC Genomics.

[67]  R. J. Herrera,et al.  The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations , 2010, European Journal of Human Genetics.

[68]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[69]  Alkes L. Price,et al.  Reconstructing Indian Population History , 2009, Nature.

[70]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[71]  Gonçalo Abecasis,et al.  Genotype-imputation accuracy across worldwide human populations. , 2009, American journal of human genetics.

[72]  Manfred Kayser,et al.  Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation , 2009, Human mutation.

[73]  R. J. Herrera,et al.  Y-chromosome diversity characterizes the Gulf of Oman , 2008, European Journal of Human Genetics.

[74]  Hanan Hamamy,et al.  Genetic disorders in the Arab world , 2006, BMJ : British Medical Journal.

[75]  R. Villems,et al.  Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. , 2004, American journal of human genetics.

[76]  P. Underhill,et al.  Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. , 2004, American journal of human genetics.

[77]  C. Tyler-Smith,et al.  Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor. , 2004, American journal of human genetics.

[78]  R. J. Herrera,et al.  The Levant versus the Horn of Africa: evidence for bidirectional corridors of human migrations. , 2004, American journal of human genetics.

[79]  Chris Tyler-Smith,et al.  The human Y chromosome: an evolutionary marker comes of age , 2003, Nature Reviews Genetics.

[80]  T. Graves,et al.  The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes , 2003, Nature.

[81]  L Rodriguez-FloresJuan,et al.  The Qatar Genome Reference: A Population-Specific Tool for Precision Medicine in the Middle East , 2016 .