David Reich

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Genetic signatures of strong recent positive selection at the lactase gene
    Todd Bersaglieri
    Divisions of Genetics and Endocrinology, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 74:1111-20. 2004
  2. pmc Reconstructing Native American population history
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 488:370-4. 2012
  3. pmc Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levels
    David Reich
    Department of Genetics, Harvard Medical School, New Research Building, Boston, MA 02115, USA
    Am J Hum Genet 80:716-26. 2007
  4. doi request reprint Genetic history of an archaic hominin group from Denisova Cave in Siberia
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 468:1053-60. 2010
  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 Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy antigen receptor for chemokines gene
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 5:e1000360. 2009
  7. pmc Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania
    David Reich
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 89:516-28. 2011
  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 Detecting natural selection by empirical comparison to random regions of the genome
    Fuli Yu
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    Hum Mol Genet 18:4853-67. 2009
  10. doi request reprint Ancient west Eurasian ancestry in southern and eastern Africa
    Joseph K Pickrell
    Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
    Proc Natl Acad Sci U S A 111:2632-7. 2014

Detail Information

Publications59

  1. pmc Genetic signatures of strong recent positive selection at the lactase gene
    Todd Bersaglieri
    Divisions of Genetics and Endocrinology, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 74:1111-20. 2004
    ....
  2. 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...
  3. pmc Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levels
    David Reich
    Department of Genetics, Harvard Medical School, New Research Building, Boston, MA 02115, USA
    Am J Hum Genet 80:716-26. 2007
    ..0x10-12 for IL-6 SR, and P<2.0x10-9 for IL-6. These results also serve as an important proof of principle, showing that admixture mapping can not only coarsely localize but can also fine map a phenotypically important variant...
  4. doi request reprint Genetic history of an archaic hominin group from Denisova Cave in Siberia
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 468:1053-60. 2010
    ..This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans...
  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 Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy antigen receptor for chemokines gene
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 5:e1000360. 2009
    ..We confirm that rs2814778 is predictive of WBC and neutrophil count in African Americans above beyond the previously described admixture association (P = 3.8 x 10(-5)), establishing a novel phenotype for this genetic variant...
  7. pmc Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania
    David Reich
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 89:516-28. 2011
    ..Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia...
  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 Detecting natural selection by empirical comparison to random regions of the genome
    Fuli Yu
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    Hum Mol Genet 18:4853-67. 2009
    ..Our study also provides a prototype for how empirical scans for ancient selection can be carried out once many genomes are sequenced...
  10. doi request reprint Ancient west Eurasian ancestry in southern and eastern Africa
    Joseph K Pickrell
    Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
    Proc Natl Acad Sci U S A 111:2632-7. 2014
    ..The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa. ..
  11. pmc Genetic evidence for recent population mixture in India
    Priya Moorjani
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Am J Hum Genet 93:422-38. 2013
    ....
  12. pmc The case for selection at CCR5-Delta32
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS Biol 3:e378. 2005
    ..More broadly, the results have general implications for the design of future studies to detect the signs of positive selection in the human genome...
  13. pmc Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men
    Matthew L Freedman
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 103:14068-73. 2006
    ..Thus, admixture mapping indicates a major, still-unidentified risk gene for prostate cancer at 8q24, motivating intense work to find it...
  14. 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...
  15. doi request reprint Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arrays
    Arti Tandon
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genet Epidemiol 35:80-3. 2011
    ..The panels provide about 80% of the maximum information about African or European ancestry, even with up to 10% missing data...
  16. 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...
  17. 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
    ....
  18. pmc Genetic differences between the determinants of lipid profile phenotypes in African and European Americans: the Jackson Heart Study
    Rahul C Deo
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    PLoS Genet 5:e1000342. 2009
    ....
  19. pmc A high-density admixture scan in 1,670 African Americans with hypertension
    Rahul C Deo
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 3:e196. 2007
    ..19 per African allele is less than what would be expected from the original report; thus, further work is needed to follow up this locus...
  20. pmc Single-nucleotide polymorphisms in LPA explain most of the ancestry-specific variation in Lp(a) levels in African Americans
    Rahul C Deo
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 6:e14581. 2011
    ..Despite the strong association with Lp(a) levels, we find no association of any LPA SNP with incident coronary heart disease in 3,225 African Americans from the Atherosclerosis Risk in Communities Study...
  21. doi request reprint The genomic landscape of Neanderthal ancestry in present-day humans
    Sriram Sankararaman
    1 Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA 2 Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 507:354-7. 2014
    ..These results suggest that part of the explanation for genomic regions of reduced Neanderthal ancestry is Neanderthal alleles that caused decreased fertility in males when moved to a modern human genetic background. ..
  22. ncbi request reprint Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens"
    Fuli Yu
    Department of Genetics, Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Science 316:370. 2007
    ..However, when we compare ASPM empirically to a large number of other loci, its variation is not unusual and does not support selection...
  23. pmc African ancestry and genetic risk for uterine leiomyomata
    Lauren A Wise
    Slone Epidemiology Center at Boston University, 1010 Commonwealth Avenue, 4th Floor, Boston, MA 02215, USA
    Am J Epidemiol 176:1159-68. 2012
    ....
  24. pmc A direct characterization of human mutation based on microsatellites
    James X Sun
    Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Genet 44:1161-5. 2012
    ..We infer that the sequence mutation rate is 1.4-2.3×10(-8) mutations per base pair per generation (90% credible interval) and that human-chimpanzee speciation occurred 3.7-6.6 million years ago...
  25. pmc Analysis of chimpanzee history based on genome sequence alignments
    Jennifer L Caswell
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 4:e1000057. 2008
    ..Study of such loci should provide information about the period of time 5-7 million years ago when the ancestors of humans separated from those of the chimpanzees...
  26. ncbi request reprint Comparison of fine-scale recombination rates in humans and chimpanzees
    Wendy Winckler
    Department of Molecular Biology and Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114 2622, USA
    Science 308:107-11. 2005
    ..Thus, local patterns of recombination rate have evolved rapidly, in a manner disproportionate to the change in DNA sequence...
  27. 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...
  28. pmc The date of interbreeding between Neandertals and modern humans
    Sriram Sankararaman
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    PLoS Genet 8:e1002947. 2012
    ..This supports the recent interbreeding hypothesis and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa...
  29. ncbi request reprint A whole-genome admixture scan finds a candidate locus for multiple sclerosis susceptibility
    David Reich
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Genet 37:1113-8. 2005
    ..We describe here the first high-powered admixture scan, focusing on 605 African American cases and 1,043 African American controls, and report a locus on chromosome 1 that is significantly associated with multiple sclerosis...
  30. pmc The difficulty of avoiding false positives in genome scans for natural selection
    Swapan Mallick
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genome Res 19:922-33. 2009
    ..Inaccuracies in the genome sequence at even a tiny fraction of genes can produce false-positive signals, which make it difficult to identify loci that have genuinely been targets of selection...
  31. pmc MHC region and risk of systemic lupus erythematosus in African American women
    Edward A Ruiz-Narváez
    Slone Epidemiology Center at Boston University, 1010 Commonwealth Avenue, Boston, MA 02215, USA
    Hum Genet 130:807-15. 2011
    ..In summary, we found four independent signals in the MHC region associated with risk of SLE in African American women...
  32. 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...
  33. 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...
  34. 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...
  35. pmc Accelerated genetic drift on chromosome X during the human dispersal out of Africa
    Alon Keinan
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 41:66-70. 2009
    ..We conclude that a sex-biased process that reduced the female effective population size, or an episode of natural selection unusually affecting chromosome X, was associated with the founding of non-African populations...
  36. pmc Human population differentiation is strongly correlated with local recombination rate
    Alon Keinan
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 6:e1000886. 2010
    ....
  37. pmc Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans
    Alon Keinan
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 39:1251-5. 2007
    ..Our analysis shows that East Asian and northern European ancestors shared the same population bottleneck expanding out of Africa but that both also experienced more recent genetic drift, which was greater in East Asians...
  38. ncbi request reprint Assessing the impact of population stratification on genetic association studies
    Matthew L Freedman
    Department of Medicine and Molecular Biology, Massachusetts General Hospital, Boston, and Program in Medical and Population Genetics, Broad Institute, Cambridge, USA
    Nat Genet 36:388-93. 2004
    ..Our results suggest that modest amounts of stratification can exist even in well designed studies...
  39. 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...
  40. pmc Population differentiation as a test for selective sweeps
    Hua Chen
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 20:393-402. 2010
    ..Our analysis identifies a list of loci as candidate targets of selection, including well-known selected loci and new regions that have not been highlighted by previous scans for selection...
  41. pmc Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants
    Nadin Rohland
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Biol 8:e1000564. 2010
    ....
  42. 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...
  43. 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
    ....
  44. pmc Reconstructing Roma history from genome-wide data
    Priya Moorjani
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 8:e58633. 2013
    ....
  45. pmc The genetic prehistory of southern Africa
    Joseph K Pickrell
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Nat Commun 3:1143. 2012
    ..In addition, the East African Hadza and Sandawe derive a fraction of their ancestry from admixture with a population related to the Khoisan, supporting the hypothesis of an ancient link between southern and eastern Africa...
  46. pmc Evidence of widespread selection on standing variation in Europe at height-associated SNPs
    Michael C Turchin
    Division of Genetics, Children s Hospital Boston, Massachusetts, USA
    Nat Genet 44:1015-9. 2012
    ..The systematic frequency differences are consistent with the presence of widespread weak selection (selection coefficients ∼10(-3)-10(-5) per allele) rather than genetic drift alone (P < 10(-15))...
  47. pmc Phasing of many thousands of genotyped samples
    Amy L Williams
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Am J Hum Genet 91:238-51. 2012
    ..Lastly, we show that HAPI-UR has better runtime scaling properties than does Beagle so that for larger data sets, HAPI-UR will be practical and will have an even larger runtime advantage. HAPI-UR is available online (see Web Resources)...
  48. pmc The role of the CD58 locus in multiple sclerosis
    Philip L De Jager
    Division of Molecular Immunology, Center for Neurologic Diseases, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 106:5264-9. 2009
    ....
  49. 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...
  50. pmc Will admixture mapping work to find disease genes?
    David Reich
    Department of Genetics, Harvard Medical School, Boston, MA, USA
    Philos Trans R Soc Lond B Biol Sci 360:1605-7. 2005
    ..We also propose a stringent criteria we believe the community should adopt before declaring a statistically significant admixture association to disease...
  51. pmc Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
    Nadin Rohland
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genome Res 22:939-46. 2012
    ..We illustrate the power and effectiveness of this approach on about 2000 samples from a prostate cancer study...
  52. 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
    ....
  53. pmc A novel approach to estimating heterozygosity from low-coverage genome sequence
    Katarzyna Bryc
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
    Genetics 195:553-61. 2013
    ..We find in practice that ratios of heterozygosity are more interpretable than absolute estimates and show that we obtain excellent conformity of ratios of heterozygosity with previous estimates from higher-coverage data. ..
  54. pmc Association studies of common variants in 10 hypogonadotropic hypogonadism genes with age at menarche
    Zofia K Z Gajdos
    Program in Genomics and Division of Endocrinology, Children s Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
    J Clin Endocrinol Metab 93:4290-8. 2008
    ..Several genes have been identified that, when mutated, cause disorders of delayed or absent puberty such as hypogonadotropic hypogonadism (HH)...
  55. ncbi request reprint Human genome sequence variation and the influence of gene history, mutation and recombination
    David E Reich
    Whitehead Institute MIT Center for Genome Research, One Kendall Square, Cambridge, Massachusetts 02139, USA
    Nat Genet 32:135-42. 2002
    ....
  56. ncbi request reprint Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia
    Penelope E Bonnen
    Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nat Genet 38:214-7. 2006
    ..The long-range LD around common alleles and limited diversity result in improved efficiency in genetic studies in this population and augments the power to detect association of 'hidden SNPs'...
  57. pmc Mapping multiple sclerosis susceptibility to the HLA-DR locus in African Americans
    Jorge R Oksenberg
    Department of Neurology, University of California at San Francisco, San Francisco, CA 94143 0435, USA
    Am J Hum Genet 74:160-7. 2004
    ..This finding is unlikely to be solely explained by admixture, since a substantial proportion of the susceptibility chromosomes from African American patients with MS displayed haplotypes consistent with an African origin...
  58. ncbi request reprint Quality and completeness of SNP databases
    David E Reich
    Program in Medical and Population Genetics, Whitehead Institute MIT Center for Genome Research, One Kendall Square, Cambridge, Massachusetts 02139, USA
    Nat Genet 33:457-8. 2003
    ..Approximately 45% of all human heterozygosity is attributable to SNPs already available from the two databases, and of SNPs with minor-allele frequencies >10%, more than half are represented...
  59. ncbi request reprint Detecting recent positive selection in the human genome from haplotype structure
    Pardis C Sabeti
    Whitehead Institute MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 419:832-7. 2002
    ..More generally, the method could be used to scan the entire genome for evidence of recent positive selection...

Research Grants9

  1. Associating genetic variation to resistance to severe malaria in East Africa
    David Reich; Fiscal Year: 2007
    ....
  2. A Whole Genome Admixture Scan for Multiple Sclerosis
    David Reich; Fiscal Year: 2007
    ..We will then move to a targeted haplotype-based association study in the most interesting regions to clone new genes associated with MS. ..
  3. Building a Latino admixture map & pilot study to find Type 2 Diabetes risk
    David Reich; Fiscal Year: 2007
    ..The study will also enable larger admixture mapping studies with many thousands of patients with Type 2 Diabetes, which we would like to pursue both in U.S. Latino and in Latin American populations. ..
  4. Population structure in whole-genome disease scans
    David Reich; Fiscal Year: 2007
    ..We believe our new techniques will provide near-optimal power, and will be computationally efficient. We intend to make all these tools publicly available for the scientific community. ..