Research Topics
Genomes and Genes
Species | David ReichSummaryAffiliation: Harvard University Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
Genetic signatures of strong recent positive selection at the lactase geneTodd Bersaglieri
Divisions of Genetics and Endocrinology, Harvard Medical School, Boston, MA 02115, USA
Am J Hum Genet 74:1111-20. 2004....
Reconstructing Native American population historyDavid 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...- Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy antigen receptor for chemokines geneDavid 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... - Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levelsDavid 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... - Reconstructing Indian population historyDavid 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... - Denisova admixture and the first modern human dispersals into Southeast Asia and OceaniaDavid 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... - Genetic history of an archaic hominin group from Denisova Cave in SiberiaDavid 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... - A genomewide admixture map for Latino populationsAlkes 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... - Detecting natural selection by empirical comparison to random regions of the genomeFuli 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... - The case for selection at CCR5-Delta32Pardis 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... - Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arraysArti 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... - The history of African gene flow into Southern Europeans, Levantines, and JewsPriya 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... - Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer ConsortiumBogdan 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... - Genetic differences between the determinants of lipid profile phenotypes in African and European Americans: the Jackson Heart StudyRahul C Deo
Department of Genetics, Harvard Medical School, Boston, MA, USA
PLoS Genet 5:e1000342. 2009.... - A high-density admixture scan in 1,670 African Americans with hypertensionRahul 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... - Sensitive detection of chromosomal segments of distinct ancestry in admixed populationsAlkes L Price
Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
PLoS Genet 5:e1000519. 2009.... - Single-nucleotide polymorphisms in LPA explain most of the ancestry-specific variation in Lp(a) levels in African AmericansRahul 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... - Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American menMatthew 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... - African ancestry and genetic risk for uterine leiomyomataLauren A Wise
Slone Epidemiology Center at Boston University, 1010 Commonwealth Avenue, 4th Floor, Boston, MA 02215, USA
Am J Epidemiol 176:1159-68. 2012.... - A direct characterization of human mutation based on microsatellitesJames 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... 
Principal components analysis corrects for stratification in genome-wide association studiesAlkes 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...- Analysis of chimpanzee history based on genome sequence alignmentsJennifer 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... - Comparison of fine-scale recombination rates in humans and chimpanzeesWendy 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... - The date of interbreeding between Neandertals and modern humansSriram 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... - The difficulty of avoiding false positives in genome scans for natural selectionSwapan 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... - MHC region and risk of systemic lupus erythematosus in African American womenEdward 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... - A whole-genome admixture scan finds a candidate locus for multiple sclerosis susceptibilityDavid 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... - 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... - Effects of cis and trans genetic ancestry on gene expression in African AmericansAlkes 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... - Discerning the ancestry of European Americans in genetic association studiesAlkes 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... - Population structure and eigenanalysisNick 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... - Accelerated genetic drift on chromosome X during the human dispersal out of AfricaAlon 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... - Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in EuropeansAlon 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... - Human population differentiation is strongly correlated with local recombination rateAlon Keinan
Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS Genet 6:e1000886. 2010.... - Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephantsNadin Rohland
Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS Biol 8:e1000564. 2010.... - Combining evidence of natural selection with association analysis increases power to detect malaria-resistance variantsGeorge 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... - The impact of divergence time on the nature of population structure: an example from IcelandAlkes L Price
Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
PLoS Genet 5:e1000505. 2009.... - Population differentiation as a test for selective sweepsHua 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... - The genetic prehistory of southern AfricaJoseph 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... - Evidence of widespread selection on standing variation in Europe at height-associated SNPsMichael 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))... - Phasing of many thousands of genotyped samplesAmy 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)... - The role of the CD58 locus in multiple sclerosisPhilip 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.... - New approaches to population stratification in genome-wide association studiesAlkes 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... - Using population admixture to help complete maps of the human genomeGiulio Genovese
1 Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 2 Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA 3 Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA 4 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Genet 45:406-14. 2013..We describe how knowledge of the locations of these sequences can inform disease association and genome biology studies... - 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... - Assessing the impact of population stratification on genetic association studiesMatthew 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... - Cost-effective, high-throughput DNA sequencing libraries for multiplexed target captureNadin 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... - Extremely low-coverage sequencing and imputation increases power for genome-wide association studiesBogdan Pasaniuc
Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
Nat Genet 44:631-5. 2012.... - Reconstructing Roma history from genome-wide dataPriya Moorjani
Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS ONE 8:e58633. 2013.... - Association studies of common variants in 10 hypogonadotropic hypogonadism genes with age at menarcheZofia 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)... - Evaluating potential for whole-genome studies in Kosrae, an isolated population in MicronesiaPenelope 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'... - Mapping multiple sclerosis susceptibility to the HLA-DR locus in African AmericansJorge 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... - Human genome sequence variation and the influence of gene history, mutation and recombinationDavid E Reich
Whitehead Institute/MIT Center for Genome Research, One Kendall Square, Cambridge, Massachusetts 02139, USA
Nat Genet 32:135-42. 2002.... - Detecting recent positive selection in the human genome from haplotype structurePardis 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... - Quality and completeness of SNP databasesDavid 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...
Research Grants
- Associating genetic variation to resistance to severe malaria in East AfricaDavid Reich; Fiscal Year: 2007....
- A Whole Genome Admixture Scan for Multiple SclerosisDavid 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. ..
- Building a Latino admixture map & pilot study to find Type 2 Diabetes riskDavid 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. ..
- Population structure in whole-genome disease scansDavid 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. ..