Alkes L Price

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Effects of cis and trans genetic ancestry on gene expression in African Americans
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS Genet 4:e1000294. 2008
  2. pmc Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS Genet 7:e1001317. 2011
  3. pmc New approaches to population stratification in genome-wide association studies
    Alkes L Price
    Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nat Rev Genet 11:459-63. 2010
  4. pmc The impact of divergence time on the nature of population structure: an example from Iceland
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
    PLoS Genet 5:e1000505. 2009
  5. pmc Reconstructing Indian population history
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 461:489-94. 2009
  6. pmc Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium
    Bogdan Pasaniuc
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    PLoS Genet 7:e1001371. 2011
  7. pmc Sensitive detection of chromosomal segments of distinct ancestry in admixed populations
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
    PLoS Genet 5:e1000519. 2009
  8. pmc A genomewide admixture map for Latino populations
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 80:1024-36. 2007
  9. pmc Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores
    Bjarni J Vilhjálmsson
    Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA 02115, USA Program in Genetic Epidemiology and Statistical Genetics, Harvard T H Chan School of Public Health, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark Electronic address
    Am J Hum Genet 97:576-92. 2015
  10. pmc Improved ancestry inference using weights from external reference panels
    Chia Yen Chen
    Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 29:1399-406. 2013

Collaborators

Detail Information

Publications48

  1. pmc Effects of cis and trans genetic ancestry on gene expression in African Americans
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS Genet 4:e1000294. 2008
    ..Both effects are highly significant, and we estimate that 12+/-3% of all heritable variation in human gene expression is due to cis variants...
  2. pmc Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS Genet 7:e1001317. 2011
    ....
  3. pmc New approaches to population stratification in genome-wide association studies
    Alkes L Price
    Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nat Rev Genet 11:459-63. 2010
    ..Here, we review recent progress on methods that correct for stratification while accounting for these additional complexities...
  4. pmc The impact of divergence time on the nature of population structure: an example from Iceland
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
    PLoS Genet 5:e1000505. 2009
    ....
  5. pmc Reconstructing Indian population history
    David Reich
    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...
  6. pmc Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium
    Bogdan Pasaniuc
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    PLoS Genet 7:e1001371. 2011
    ..Our methods and our publicly available software are broadly applicable to GWAS in admixed populations...
  7. pmc Sensitive detection of chromosomal segments of distinct ancestry in admixed populations
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
    PLoS Genet 5:e1000519. 2009
    ....
  8. pmc A genomewide admixture map for Latino populations
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 80:1024-36. 2007
    ..We evaluated the effectiveness of our map for localizing disease genes in four Latino populations from both North and South America...
  9. pmc Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores
    Bjarni J Vilhjálmsson
    Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA 02115, USA Program in Genetic Epidemiology and Statistical Genetics, Harvard T H Chan School of Public Health, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark Electronic address
    Am J Hum Genet 97:576-92. 2015
    ..A similar relative improvement in accuracy was observed for three additional large disease datasets and for non-European schizophrenia samples. The advantage of LDpred over existing methods will grow as sample sizes increase. ..
  10. pmc Improved ancestry inference using weights from external reference panels
    Chia Yen Chen
    Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 29:1399-406. 2013
    ....
  11. pmc Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection
    Gaurav Bhatia
    Harvard Massachusetts Institute of Technology MIT Division of Health, Science and Technology, Cambridge, USA
    Am J Hum Genet 89:368-81. 2011
    ..The most significantly differentiated marker in our analysis, rs2920283, is highly differentiated in both Africa and East Asia and has prior genome-wide significant associations to bladder and gastric cancers...
  12. pmc Partitioning heritability by functional annotation using genome-wide association summary statistics
    Hilary K Finucane
    Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Genet 47:1228-35. 2015
    ....
  13. pmc Informed conditioning on clinical covariates increases power in case-control association studies
    Noah Zaitlen
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS Genet 8:e1003032. 2012
    ..This suggests that applying our method to existing and future association studies of these diseases may identify novel disease loci...
  14. pmc The history of African gene flow into Southern Europeans, Levantines, and Jews
    Priya Moorjani
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 7:e1001373. 2011
    ..For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas...
  15. pmc Two independent alleles at 6q23 associated with risk of rheumatoid arthritis
    Robert M Plenge
    Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nat Genet 39:1477-82. 2007
    ..We show that these two SNP associations are statistically independent, are each reproducible in the comparison of our data and WTCCC data, and define risk and protective haplotypes for rheumatoid arthritis at 6q23...
  16. pmc Population structure and eigenanalysis
    Nick Patterson
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
    PLoS Genet 2:e190. 2006
    ..This means that we can predict the dataset size needed to detect structure...
  17. pmc Discerning the ancestry of European Americans in genetic association studies
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 4:e236. 2008
    ..We demonstrate that this panel of markers can be used to correct for stratification in association studies that do not generate dense genotype data...
  18. pmc Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates
    Pier Francesco Palamara
    Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Electronic address
    Am J Hum Genet 97:775-89. 2015
    ..Our analysis suggests that a mutation-rate estimate higher than that reported by recent pedigree-based studies should be adopted in the context of DNA-based demographic reconstruction...
  19. pmc Fast and accurate imputation of summary statistics enhances evidence of functional enrichment
    Bogdan Pasaniuc
    Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90024, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, 90024, Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, 94143, Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, 02115, Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA, 02115, Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, Department of Genetics Harvard Medical School, Boston, MA, 02115 and Division of Population Health Sciences and Education, St George s, University of London, UK Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90024, Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, 90024, Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, 94143, Program in Genetic Epidemiology and Statistical Genetics, France
    Bioinformatics 30:2906-14. 2014
    ..Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available...
  20. pmc Replication and fine mapping of asthma-associated loci in individuals of African ancestry
    David B Kantor
    Division of Critical Care Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children s Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
    Hum Genet 132:1039-47. 2013
    ..These results improve the understanding of asthma genetics and further demonstrate the utility of genetic studies in populations other than those of largely European ancestry. ..
  21. pmc Using population admixture to help complete maps of the human genome
    Giulio Genovese
    Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Genet 45:406-14, 414e1-2. 2013
    ..We describe how knowledge of the locations of these sequences can inform disease association and genome biology studies...
  22. pmc Analysis of case-control association studies with known risk variants
    Noah Zaitlen
    Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 28:1729-37. 2012
    ..Roughly, this method estimates model parameters for each known variant while accounting for the published disease prevalence from the epidemiological literature...
  23. pmc Pooled association tests for rare variants in exon-resequencing studies
    Alkes L Price
    Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
    Am J Hum Genet 86:832-8. 2010
    ..We used a rigorous population-genetics simulation framework to evaluate the power of the method, and we applied the method to empirical sequencing data from three disease studies...
  24. pmc Population Structure of UK Biobank and Ancient Eurasians Reveals Adaptation at Genes Influencing Blood Pressure
    Kevin J Galinsky
    Department of Biostatistics, Harvard T H Chan School of Public Health, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Electronic address
    Am J Hum Genet 99:1130-1139. 2016
    ..10 × 10-19) and the variants with ancient Eurasian selection signals at the ATXN2-SH2B3 locus (p = 8.00 × 10-33), implicating recent adaptation related to blood pressure...
  25. pmc Deep targeted sequencing of 12 breast cancer susceptibility regions in 4611 women across four different ethnicities
    Sara Lindstrom
    Department of Epidemiology, University of Washington, 1959 N E Pacific Street, Health Sciences Building, Room F247B, Seattle, WA, 98195, USA
    Breast Cancer Res 18:109. 2016
    ..It is likely that the GWAS signal originates from one or many as yet unidentified causal variants...
  26. pmc Two-Variance-Component Model Improves Genetic Prediction in Family Datasets
    George Tucker
    Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Epidemiology, Harvard T H Chan School of Public Health, Harvard University, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Am J Hum Genet 97:677-90. 2015
    ..We also find that standard mixed-model association tests can produce inflated test statistics in datasets with related individuals, whereas the two-variance-component model corrects for inflation. ..
  27. pmc Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis
    Po Ru Loh
    Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, Massachusetts, USA
    Nat Genet 47:1385-92. 2015
    ..To accomplish these analyses, we developed a fast algorithm for multicomponent, multi-trait variance-components analysis that overcomes prior computational barriers that made such analyses intractable at this scale. ..
  28. pmc Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia
    Kevin J Galinsky
    Department of Biostatistics, Harvard T H Chan School of Public Health, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Electronic address
    Am J Hum Genet 98:456-72. 2016
    ..We also detect selection signals at IGFBP3 and IGH, which have also previously been associated to human disease...
  29. pmc An atlas of genetic correlations across human diseases and traits
    Brendan Bulik-Sullivan
    Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Genet 47:1236-41. 2015
    ..These results highlight the power of genome-wide analyses, as there currently are no significantly associated SNPs for anorexia nervosa and only three for educational attainment. ..
  30. pmc Mixed model with correction for case-control ascertainment increases association power
    Tristan J Hayeck
    Department of Biostatistics, Harvard T H Chan School of Public Health, Harvard University, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Electronic address
    Am J Hum Genet 96:720-30. 2015
    ..Larger increases in power are expected at larger sample sizes. In conclusion, case-control studies of diseases with low prevalence can achieve power higher than that in existing mixed-model methods...
  31. pmc Efficient Bayesian mixed-model analysis increases association power in large cohorts
    Po Ru Loh
    1 Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, Massachusetts, USA 2 Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Genet 47:284-90. 2015
    ..Theory and simulations show that the boost in power increases with cohort size, making BOLT-LMM appealing for genome-wide association studies in large cohorts. ..
  32. pmc LD Score regression distinguishes confounding from polygenicity in genome-wide association studies
    Brendan K Bulik-Sullivan
    1 Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 2 Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA 3 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Genet 47:291-5. 2015
    ..We find strong evidence that polygenicity accounts for the majority of the inflation in test statistics in many GWAS of large sample size. ..
  33. pmc Reconstructing Native American population history
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 488:370-4. 2012
    ..A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America...
  34. pmc Combining evidence of natural selection with association analysis increases power to detect malaria-resistance variants
    George Ayodo
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 81:234-42. 2007
    ..This empirically demonstrates that combining association analysis with evidence of natural selection can increase power to detect risk variants by orders of magnitude--up to P=.000018 for HBB and P=.00043 for CD36...
  35. pmc Explicit Modeling of Ancestry Improves Polygenic Risk Scores and BLUP Prediction
    Chia Yen Chen
    Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, Massachusetts, United States of America
    Genet Epidemiol 39:427-38. 2015
    ..In summary, our results show that explicitly modeling ancestry can be important in both PRS and BLUP prediction...
  36. pmc Fast and accurate long-range phasing in a UK Biobank cohort
    Po Ru Loh
    Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, Massachusetts, USA
    Nat Genet 48:811-6. 2016
    ....
  37. pmc Integrative approaches for large-scale transcriptome-wide association studies
    Alexander Gusev
    Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, Massachusetts, USA
    Nat Genet 48:245-52. 2016
    ..Our results showcase the power of integrating genotype, gene expression and phenotype to gain insights into the genetic basis of complex traits...
  38. pmc Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture
    Gaurav Bhatia
    Division of Health, Science, and Technology, The Harvard MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA Electronic address
    Am J Hum Genet 95:437-44. 2014
    ....
  39. pmc Adjusting for heritable covariates can bias effect estimates in genome-wide association studies
    Hugues Aschard
    Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA Electronic address
    Am J Hum Genet 96:329-39. 2015
    ..Using both theory and simulations, we explore this phenomenon in detail and discuss the ramifications for future genome-wide association studies of correlated traits and diseases. ..
  40. pmc Estimating and interpreting FST: the impact of rare variants
    Gaurav Bhatia
    Harvard Massachusetts Institute of Technology MIT, Division of Health, Science, and Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 23:1514-21. 2013
    ..Changes in each of these aspects of estimation may result in FST estimates that are highly divergent from one another. Here, we clarify these issues and propose solutions. ..
  41. pmc Genetic variation in RNASEL associated with prostate cancer risk and progression
    Mara S Meyer
    Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
    Carcinogenesis 31:1597-603. 2010
    ..The results of this study support a link between RNASEL and prostate cancer and suggest that the association may be mediated through inflammation. These novel findings warrant replication in future studies...
  42. ncbi request reprint 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...
  43. pmc Integrating common and rare genetic variation in diverse human populations
    David M Altshuler
    Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA
    Nature 467:52-8. 2010
    ....
  44. pmc Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation
    Alexander Gusev
    Program in Genetic Epidemiology and Statistical Genetics, Harvard T H Chan School of Public Health, Boston, Massachusetts 02115, USA
    Nat Commun 7:10979. 2016
    ..Our findings showcase the power of integrating functional annotation with genetic data to understand the genetic basis of PrCa. ..
  45. pmc Abundant contribution of short tandem repeats to gene expression variation in humans
    Melissa Gymrek
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
    Nat Genet 48:22-9. 2016
    ..These results highlight the contribution of STRs to the genetic architecture of quantitative human traits. ..
  46. pmc Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases
    Alexander Gusev
    Harvard School of Public Health, Boston, MA 02115, USA Electronic address
    Am J Hum Genet 95:535-52. 2014
    ..Our results highlight the value of analyzing components of heritability to unravel the functional architecture of common disease. ..
  47. pmc Quantifying missing heritability at known GWAS loci
    Alexander Gusev
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America
    PLoS Genet 9:e1003993. 2013
    ..These findings have important ramifications for fine-mapping study design and our understanding of complex disease architecture...
  48. pmc Extremely low-coverage sequencing and imputation increases power for genome-wide association studies
    Bogdan Pasaniuc
    Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    Nat Genet 44:631-5. 2012
    ....

Research Grants1

  1. Diverse implications of population structure for identifying human disease genes
    Alkes Price; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..