Jonathan Pritchard

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. pmc 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
  2. pmc Adaptations to climate in candidate genes for common metabolic disorders
    Angela M Hancock
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 4:e32. 2008
  3. pmc Gene expression levels are a target of recent natural selection in the human genome
    Sridhar Kudaravalli
    Department of Human Genetics, The University of Chicago, USA
    Mol Biol Evol 26:649-58. 2009
  4. pmc Dissecting the regulatory architecture of gene expression QTLs
    Daniel J Gaffney
    Department of Human Genetics, University of Chicago, 920 E58th Street, Chicago, IL 60637, USA
    Genome Biol 13:R7. 2012
  5. pmc 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
  6. pmc Efficient counting of k-mers in DNA sequences using a bloom filter
    Páll Melsted
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    BMC Bioinformatics 12:333. 2011
  7. pmc The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation
    Jonathan 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
  8. ncbi request reprint 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
  9. doi request reprint Adaptation - not by sweeps alone
    Jonathan K Pritchard
    Department of Human Genetics, Howard Hughes Medical Institute, University of Chicago, Illinois 60615, USA
    Nat Rev Genet 11:665-7. 2010
  10. pmc Statistical tests for admixture mapping with case-control and cases-only data
    Giovanni Montana
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 75:771-89. 2004

Detail Information

Publications39

  1. pmc 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...
  2. pmc Adaptations to climate in candidate genes for common metabolic disorders
    Angela 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...
  3. pmc Gene expression levels are a target of recent natural selection in the human genome
    Sridhar Kudaravalli
    Department of Human Genetics, The University of Chicago, USA
    Mol Biol Evol 26:649-58. 2009
    ....
  4. pmc Dissecting the regulatory architecture of gene expression QTLs
    Daniel 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...
  5. pmc 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...
  6. pmc Efficient counting of k-mers in DNA sequences using a bloom filter
    Páll 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...
  7. pmc The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation
    Jonathan 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...
  8. ncbi request reprint 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...
  9. doi request reprint Adaptation - not by sweeps alone
    Jonathan K Pritchard
    Department of Human Genetics, Howard Hughes Medical Institute, University of Chicago, Illinois 60615, USA
    Nat Rev Genet 11:665-7. 2010
    There 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 ..
  10. pmc Statistical tests for admixture mapping with case-control and cases-only data
    Giovanni 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...
  11. pmc 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...
  12. ncbi request reprint A worldwide survey of haplotype variation and linkage disequilibrium in the human genome
    Donald 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...
  13. pmc Characterizing natural variation using next-generation sequencing technologies
    Yoav 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...
  14. ncbi request reprint High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans
    Graham 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...
  15. pmc 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
    ..Finally, we search for local adaptation between geographically close populations, and highlight several examples...
  16. pmc Revealing the architecture of gene regulation: the promise of eQTL studies
    Yoav Gilad
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Trends Genet 24:408-15. 2008
    ....
  17. ncbi request reprint Haplotype blocks and linkage disequilibrium in the human genome
    Jeffrey 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...
  18. pmc Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
    Jacob 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)...
  19. pmc Assessing the performance of the haplotype block model of linkage disequilibrium
    Jeffrey D Wall
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    Am J Hum Genet 73:502-15. 2003
    ....
  20. pmc Understanding mechanisms underlying human gene expression variation with RNA sequencing
    Joseph 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...
  21. pmc Clines, clusters, and the effect of study design on the inference of human population structure
    Noah 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
    ....
  22. pmc Confounding from cryptic relatedness in case-control association studies
    Benjamin 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...
  23. pmc Association mapping and fine mapping with TreeLD
    Sebastian 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...
  24. pmc Coalescent-based association mapping and fine mapping of complex trait loci
    Sebastian 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)...
  25. pmc Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency
    Angela M Hancock
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 107:8924-30. 2010
    ....
  26. pmc The role of geography in human adaptation
    Graham 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...
  27. pmc Evidence for extensive transmission distortion in the human genome
    Sebastian 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...
  28. ncbi request reprint A high-resolution survey of deletion polymorphism in the human genome
    Donald 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...
  29. pmc A statistical framework for joint eQTL analysis in multiple tissues
    Timothée Flutre
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 9:e1003486. 2013
    ..05). Further, the results suggest that, in contrast to previous analyses of the same data, the majority of eQTLs detectable in these data are shared among all three tissues...
  30. pmc Adaptive evolution of conserved noncoding elements in mammals
    Su 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...
  31. ncbi request reprint Genetic structure of human populations
    Noah 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...
  32. ncbi request reprint Traces of human migrations in Helicobacter pylori populations
    Daniel Falush
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, 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...
  33. pmc Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    Daniel 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...
  34. pmc Informativeness of genetic markers for inference of ancestry
    Noah 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...
  35. pmc Overcoming the winner's curse: estimating penetrance parameters from case-control data
    Sebastian 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...
  36. pmc Completing the map of human genetic variation
    Evan E Eichler
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 447:161-5. 2007
  37. pmc Sequencing and analysis of Neanderthal genomic DNA
    James 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...
  38. pmc Convergent adaptation of human lactase persistence in Africa and Europe
    Sarah 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...
  39. pmc Clonal origin and evolution of a transmissible cancer
    Claudio 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 Grants10

  1. Linkage Disequilibrium Methods For Complex Trait Mapping
    Jonathan Pritchard; Fiscal Year: 2003
    ..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. ..
  2. 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. ..
  3. Analysis and interpretation of DNA Sequence Data in Association Studies
    Jonathan 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. ..
  4. Analysis and interpretation of DNA Sequence Data in Association Studies
    Jonathan Pritchard; Fiscal Year: 2009
    ..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. ..
  5. Linkage Disequilibrium Methods For Complex Trait Mapping
    Jonathan 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. ..
  6. Linkage Disequilibrium Methods For Complex Trait Mapping
    Jonathan Pritchard; Fiscal Year: 2006
    ..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. ..
  7. Linkage Disequilibrium Methods For Complex Trait Mapping
    Jonathan Pritchard; Fiscal Year: 2005
    ..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. ..
  8. Linkage Disequilibrium Methods For Complex Trait Mapping
    Jonathan Pritchard; Fiscal Year: 2004
    ..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. ..
  9. Analysis and interpretation of DNA Sequence Data in Association Studies
    Jonathan K Pritchard; Fiscal Year: 2010
    ..abstract_text> ..