Research Topics
| Jonathan PritchardSummaryAffiliation: University of Chicago Country: USA Publications
Research Grants
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Detail Information
Publications
A map of recent positive selection in the human genomeBenjamin 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...- Adaptations to climate in candidate genes for common metabolic disordersAngela M Hancock
Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
PLoS Genet 4:e32. 2008..Nevertheless, our results are consistent with the idea that climate has been an important selective pressure acting on candidate genes for common metabolic disorders... - Dissecting the regulatory architecture of gene expression QTLsDaniel J Gaffney
Department of Human Genetics, University of Chicago, 920 E58th Street, Chicago, IL 60637, USA
Genome Biol 13:R7. 2012..Using the HapMap lymphoblastoid cell lines, we combine 1000 Genomes genotypes and an extensive catalogue of human functional elements to investigate the biological mechanisms that eQTLs perturb... - DNA methylation patterns associate with genetic and gene expression variation in HapMap cell linesJordana 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... - Efficient counting of k-mers in DNA sequences using a bloom filterPáll Melsted
Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
BMC Bioinformatics 12:333. 2011..These singleton k-mers are uninformative for many algorithms without some kind of error correction... 
Adaptation - not by sweeps aloneJonathan K Pritchard
Department of Human Genetics, Howard Hughes Medical Institute, University of Chicago, Illinois 60615, USA
Nat Rev Genet 11:665-7. 2010There has been recent progress in identifying selective sweeps underlying a range of adaptations. Jonathan Pritchard and Anna Di Rienzo argue that many adaptive events in natural populations may occur by polygenic adaptation, which would ..- The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptationJonathan K Pritchard
Department of Human Genetics, The University of Chicago, Room 507, 929 E 58th St, Chicago, IL 60637, USA
Curr Biol 20:R208-15. 2010..We close by discussing some of the likely opportunities for progress in the field... 
The allelic architecture of human disease genes: common disease-common variant...or not?Jonathan K Pritchard
Department of Human Genetics, University of Chicago, 920 E 58th St CLSC 507, Chicago IL 60637, USA
Hum Mol Genet 11:2417-23. 2002..We also show that the predicted frequency spectrum of disease variants at a gene depends crucially on the method of ascertainment, for example from prior linkage scans or from surveys of functional candidate loci...- Statistical tests for admixture mapping with case-control and cases-only dataGiovanni Montana
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Am J Hum Genet 75:771-89. 2004..Software to perform the gene-mapping calculations, "MALDsoft," is freely available on the Pritchard Lab Web site... - High-resolution mapping of expression-QTLs yields insight into human gene regulationJean 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... - A worldwide survey of haplotype variation and linkage disequilibrium in the human genomeDonald F Conrad
Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Genet 38:1251-60. 2006..Consequently, although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HapMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations... - Gene expression levels are a target of recent natural selection in the human genomeSridhar Kudaravalli
Department of Human Genetics, The University of Chicago, USA
Mol Biol Evol 26:649-58. 2009.... - Signals of recent positive selection in a worldwide sample of human populationsJoseph K Pickrell
Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
Genome Res 19:826-37. 2009..Finally, we search for local adaptation between geographically close populations, and highlight several examples... - Characterizing natural variation using next-generation sequencing technologiesYoav Gilad
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Trends Genet 25:463-71. 2009..A better understanding of the sources of error and bias in sequencing data is essential, especially in the context of studies of variation at dynamic quantitative traits... - Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing dataJacob F Degner
Department of Human Genetics, University of Chicago, 920 E 58th St, CLSC 507, Chicago, IL 60637, USA
Bioinformatics 25:3207-12. 2009..Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE)... - High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humansGraham Coop
Department of Human Genetics, University of Chicago, 920 East 58th Street, Cummings Life Science Center, Chicago, IL 60637, USA
Science 319:1395-8. 2008..Notably, however, we found extensive and heritable variation among both males and females in the proportion of crossovers occurring in these hotspots... - Assessing the performance of the haplotype block model of linkage disequilibriumJeffrey D Wall
Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
Am J Hum Genet 73:502-15. 2003.... - Understanding mechanisms underlying human gene expression variation with RNA sequencingJoseph K Pickrell
Department of Human Genetics, The University of Chicago, Chicago 60637, USA
Nature 464:768-72. 2010..Our results illustrate the power of high-throughput sequencing for the joint analysis of variation in transcription, splicing and allele-specific expression across individuals... - Clines, clusters, and the effect of study design on the inference of human population structureNoah A Rosenberg
Department of Human Genetics, Bioinformatics Program, and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
PLoS Genet 1:e70. 2005.... - Haplotype blocks and linkage disequilibrium in the human genomeJeffrey D Wall
Department of Human Genetics, The University of Chicago, 920 East 58th Street, CLSC 507, Chicago, Illinois 60637, USA
Nat Rev Genet 4:587-97. 2003..Here, we review recent developments in this field, including the recently proposed 'haplotype-block' model of LD. We describe some of the recent data in detail and compare the observed patterns to those seen in simulations... - Confounding from cryptic relatedness in case-control association studiesBenjamin F Voight
Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
PLoS Genet 1:e32. 2005..As an example, we analyze the impact of excess relatedness among cases for six phenotypes measured in the Hutterite population... - Association mapping and fine mapping with TreeLDSebastian Zollner
Department of Human Genetics, The University of Chicago 920 East 58th Street CLSC 507, Chicago, IL 60637, USA
Bioinformatics 21:3168-70. 2005..TreeLD provides an easy-to-use interface and can be applied to case-control, TDT trio and quantitative trait data... - Coalescent-based association mapping and fine mapping of complex trait lociSebastian Zollner
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genetics 169:1071-92. 2005..We describe applications of the method to simulated data and to data from a Mendelian locus (CFTR, responsible for cystic fibrosis) and from a proposed complex trait locus (calpain-10, implicated in type 2 diabetes)... - Revealing the architecture of gene regulation: the promise of eQTL studiesYoav Gilad
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Trends Genet 24:408-15. 2008.... - The role of geography in human adaptationGraham Coop
Department of Human Genetics, University of Chicago, Chicago, IL, USA
PLoS Genet 5:e1000500. 2009..These patterns suggest that selection is often weak enough that neutral processes -- especially population history, migration, and drift -- exert powerful influences over the fate and geographic distribution of selected alleles... - Evidence for extensive transmission distortion in the human genomeSebastian Zollner
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Am J Hum Genet 74:62-72. 2004..Finally, our results also have implications for mapping disease genes and for the genetics of fertility... - Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequencyAngela M Hancock
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Proc Natl Acad Sci U S A 107:8924-30. 2010.... - A high-resolution survey of deletion polymorphism in the human genomeDonald F Conrad
Department of Human Genetics, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Genet 38:75-81. 2006..Our new method will permit the identification of deletion polymorphisms in high-density SNP surveys of trio or other family data... - Adaptive evolution of conserved noncoding elements in mammalsSu Yeon Kim
Department of Statistics, The University of Chicago, Chicago, Illinois, USA
PLoS Genet 3:1572-86. 2007..Our analyses suggest a large set of promising targets for future functional studies of adaptation... - Genetic structure of human populationsNoah A Rosenberg
Molecular and Computational Biology, 1042 West 36th Place DRB 289, University of Southern California, Los Angeles, CA 90089, USA
Science 298:2381-5. 2002..General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies... - Traces of human migrations in Helicobacter pylori populationsDaniel Falush
Department of Molecular Biology, , 10117 Berlin, Germany
Science 299:1582-5. 2003..Subsequent spread can be attributed to human migratory fluxes such as the prehistoric colonization of Polynesia and the Americas, the neolithic introduction of farming to Europe, the Bantu expansion within Africa, and the slave trade... - Informativeness of genetic markers for inference of ancestryNoah A Rosenberg
Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
Am J Hum Genet 73:1402-22. 2003..Our results can aid in decisions about the type, quantity, and specific choice of markers for use in studies of ancestry... - Overcoming the winner's curse: estimating penetrance parameters from case-control dataSebastian Zollner
Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
Am J Hum Genet 80:605-15. 2007..Finally, we show that application of the method to case-control data can improve the design of replication studies considerably... - Inference of population structure using multilocus genotype data: linked loci and correlated allele frequenciesDaniel Falush
Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, Schumann Strasse 21 22, 10117 Berlin, Germany
Genetics 164:1567-87. 2003..The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu... - Completing the map of human genetic variationEvan E Eichler
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Nature 447:161-5. 2007 - Sequencing and analysis of Neanderthal genomic DNAJames P Noonan
U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
Science 314:1113-8. 2006..This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics... - Convergent adaptation of human lactase persistence in Africa and EuropeSarah A Tishkoff
Department of Biology, University of Maryland, College Park, Maryland 20742, USA
Nat Genet 39:31-40. 2007..These data provide a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits-animal domestication and adult milk consumption... - Clonal origin and evolution of a transmissible cancerClaudio Murgia
MRC UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 46 Cleveland Street, London W1T 4JF, UK
Cell 126:477-87. 2006..Our findings have implications for understanding genome instability in cancer, natural transplantation of allografts, and the capacity of a somatic cell to evolve into a transmissible parasite...
Research Grants
- Statistical analysis of gene expression quantitative trait loci (eQTL)Jonathan K Pritchard; Fiscal Year: 2010..We will develop analytical tools for both microarray-based and RNA-sequence-based measurements of gene expression. ..
- Analysis and interpretation of DNA Sequence Data in Association StudiesJonathan K Pritchard; Fiscal Year: 2010..Using, in part, our improved functional annotation of potentially functional sites, we will also develop new statistical methods to identify genes that contribute to disease phenotypes through the action of many rare variants. ..
- Linkage Disequilibrium Methods For Complex Trait MappingJonathan Pritchard; Fiscal Year: 2007..The long term goal of this project is to develop statistical/computational tools and models of LD that can be of practical use to complex trait mapping community, and will contribute to cheaper and more effective studies. ..
- Analysis and interpretation of DNA Sequence Data in Association StudiesJonathan K Pritchard; Fiscal Year: 2010..abstract_text> ..