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  • Europe/ethnology  (3)
  • Nature Publishing Group (NPG)  (3)
  • American Geophysical Union (AGU)
  • Institute of Physics
  • Springer
  • 2005-2009  (3)
  • 1935-1939
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  • Nature Publishing Group (NPG)  (3)
  • American Geophysical Union (AGU)
  • Institute of Physics
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  • 1
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    Proportionally more deleterious genetic variation in European than in African populations (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-02-22
    Description: Quantifying the number of deleterious mutations per diploid human genome is of crucial concern to both evolutionary and medical geneticists. Here we combine genome-wide polymorphism data from PCR-based exon resequencing, comparative genomic data across mammalian species, and protein structure predictions to estimate the number of functionally consequential single-nucleotide polymorphisms (SNPs) carried by each of 15 African American (AA) and 20 European American (EA) individuals. We find that AAs show significantly higher levels of nucleotide heterozygosity than do EAs for all categories of functional SNPs considered, including synonymous, non-synonymous, predicted 'benign', predicted 'possibly damaging' and predicted 'probably damaging' SNPs. This result is wholly consistent with previous work showing higher overall levels of nucleotide variation in African populations than in Europeans. EA individuals, in contrast, have significantly more genotypes homozygous for the derived allele at synonymous and non-synonymous SNPs and for the damaging allele at 'probably damaging' SNPs than AAs do. For SNPs segregating only in one population or the other, the proportion of non-synonymous SNPs is significantly higher in the EA sample (55.4%) than in the AA sample (47.0%; P 〈 2.3 x 10(-37)). We observe a similar proportional excess of SNPs that are inferred to be 'probably damaging' (15.9% in EA; 12.1% in AA; P 〈 3.3 x 10(-11)). Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923434/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923434/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lohmueller, Kirk E -- Indap, Amit R -- Schmidt, Steffen -- Boyko, Adam R -- Hernandez, Ryan D -- Hubisz, Melissa J -- Sninsky, John J -- White, Thomas J -- Sunyaev, Shamil R -- Nielsen, Rasmus -- Clark, Andrew G -- Bustamante, Carlos D -- P50 GM065509/GM/NIGMS NIH HHS/ -- P50 GM065509-070006/GM/NIGMS NIH HHS/ -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 HG003229-03/HG/NHGRI NIH HHS/ -- R01 HL072904/HL/NHLBI NIH HHS/ -- England -- Nature. 2008 Feb 21;451(7181):994-7. doi: 10.1038/nature06611.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18288194" target="_blank"〉PubMed〈/a〉
    Keywords: Africa/ethnology ; Alleles ; Computational Biology ; Emigration and Immigration ; Europe/ethnology ; Exons/genetics ; Genome, Human/*genetics ; Heterozygote ; Homozygote ; Humans ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/*genetics ; United States
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-08-18
    Description: Chronic infection with hepatitis C virus (HCV) affects 170 million people worldwide and is the leading cause of cirrhosis in North America. Although the recommended treatment for chronic infection involves a 48-week course of peginterferon-alpha-2b (PegIFN-alpha-2b) or -alpha-2a (PegIFN-alpha-2a) combined with ribavirin (RBV), it is well known that many patients will not be cured by treatment, and that patients of European ancestry have a significantly higher probability of being cured than patients of African ancestry. In addition to limited efficacy, treatment is often poorly tolerated because of side effects that prevent some patients from completing therapy. For these reasons, identification of the determinants of response to treatment is a high priority. Here we report that a genetic polymorphism near the IL28B gene, encoding interferon-lambda-3 (IFN-lambda-3), is associated with an approximately twofold change in response to treatment, both among patients of European ancestry (P = 1.06 x 10(-25)) and African-Americans (P = 2.06 x 10(-3)). Because the genotype leading to better response is in substantially greater frequency in European than African populations, this genetic polymorphism also explains approximately half of the difference in response rates between African-Americans and patients of European ancestry.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ge, Dongliang -- Fellay, Jacques -- Thompson, Alexander J -- Simon, Jason S -- Shianna, Kevin V -- Urban, Thomas J -- Heinzen, Erin L -- Qiu, Ping -- Bertelsen, Arthur H -- Muir, Andrew J -- Sulkowski, Mark -- McHutchison, John G -- Goldstein, David B -- England -- Nature. 2009 Sep 17;461(7262):399-401. doi: 10.1038/nature08309. Epub 2009 Aug 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genome Sciences & Policy, Center for Human Genome Variation, Duke University, Durham, North Carolina 27708, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19684573" target="_blank"〉PubMed〈/a〉
    Keywords: African Americans/genetics ; Chromosomes, Human, Pair 19/genetics ; Clinical Trials as Topic ; Europe/ethnology ; Far East/ethnology ; Gene Frequency ; Genetic Variation/*genetics ; Genome, Human/genetics ; Genome-Wide Association Study ; Genotype ; Hepacivirus/*drug effects ; Hepatitis C, Chronic/*drug therapy/ethnology/*genetics/virology ; Hispanic Americans/genetics ; Humans ; Interferon-alpha/adverse effects/*pharmacology/therapeutic use ; Interleukins/*genetics ; Pharmacogenetics ; Polyethylene Glycols/adverse effects/*pharmacology/therapeutic use ; Polymorphism, Single Nucleotide/genetics ; Recombinant Proteins ; *Viral Load
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Autism genome-wide copy number variation reveals ubiquitin and neuronal genes (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-05-01
    Description: Autism spectrum disorders (ASDs) are childhood neurodevelopmental disorders with complex genetic origins. Previous studies focusing on candidate genes or genomic regions have identified several copy number variations (CNVs) that are associated with an increased risk of ASDs. Here we present the results from a whole-genome CNV study on a cohort of 859 ASD cases and 1,409 healthy children of European ancestry who were genotyped with approximately 550,000 single nucleotide polymorphism markers, in an attempt to comprehensively identify CNVs conferring susceptibility to ASDs. Positive findings were evaluated in an independent cohort of 1,336 ASD cases and 1,110 controls of European ancestry. Besides previously reported ASD candidate genes, such as NRXN1 (ref. 10) and CNTN4 (refs 11, 12), several new susceptibility genes encoding neuronal cell-adhesion molecules, including NLGN1 and ASTN2, were enriched with CNVs in ASD cases compared to controls (P = 9.5 x 10(-3)). Furthermore, CNVs within or surrounding genes involved in the ubiquitin pathways, including UBE3A, PARK2, RFWD2 and FBXO40, were affected by CNVs not observed in controls (P = 3.3 x 10(-3)). We also identified duplications 55 kilobases upstream of complementary DNA AK123120 (P = 3.6 x 10(-6)). Although these variants may be individually rare, they target genes involved in neuronal cell-adhesion or ubiquitin degradation, indicating that these two important gene networks expressed within the central nervous system may contribute to the genetic susceptibility of ASD.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925224/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925224/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Glessner, Joseph T -- Wang, Kai -- Cai, Guiqing -- Korvatska, Olena -- Kim, Cecilia E -- Wood, Shawn -- Zhang, Haitao -- Estes, Annette -- Brune, Camille W -- Bradfield, Jonathan P -- Imielinski, Marcin -- Frackelton, Edward C -- Reichert, Jennifer -- Crawford, Emily L -- Munson, Jeffrey -- Sleiman, Patrick M A -- Chiavacci, Rosetta -- Annaiah, Kiran -- Thomas, Kelly -- Hou, Cuiping -- Glaberson, Wendy -- Flory, James -- Otieno, Frederick -- Garris, Maria -- Soorya, Latha -- Klei, Lambertus -- Piven, Joseph -- Meyer, Kacie J -- Anagnostou, Evdokia -- Sakurai, Takeshi -- Game, Rachel M -- Rudd, Danielle S -- Zurawiecki, Danielle -- McDougle, Christopher J -- Davis, Lea K -- Miller, Judith -- Posey, David J -- Michaels, Shana -- Kolevzon, Alexander -- Silverman, Jeremy M -- Bernier, Raphael -- Levy, Susan E -- Schultz, Robert T -- Dawson, Geraldine -- Owley, Thomas -- McMahon, William M -- Wassink, Thomas H -- Sweeney, John A -- Nurnberger, John I -- Coon, Hilary -- Sutcliffe, James S -- Minshew, Nancy J -- Grant, Struan F A -- Bucan, Maja -- Cook, Edwin H -- Buxbaum, Joseph D -- Devlin, Bernie -- Schellenberg, Gerard D -- Hakonarson, Hakon -- 1U24MH081810/MH/NIMH NIH HHS/ -- HD055751/HD/NICHD NIH HHS/ -- HD055782-01/HD/NICHD NIH HHS/ -- HD35476/HD/NICHD NIH HHS/ -- M01 RR000064-340579/RR/NCRR NIH HHS/ -- M01 RR000064-350579/RR/NCRR NIH HHS/ -- M01 RR000064-35S10579/RR/NCRR NIH HHS/ -- M01 RR000064-35S10591/RR/NCRR NIH HHS/ -- M01 RR000064-35S10602/RR/NCRR NIH HHS/ -- M01 RR000064-35S20579/RR/NCRR NIH HHS/ -- M01 RR000064-35S20591/RR/NCRR NIH HHS/ -- M01 RR000064-35S20602/RR/NCRR NIH HHS/ -- M01 RR000064-360579/RR/NCRR NIH HHS/ -- M01 RR000064-360582/RR/NCRR NIH HHS/ -- M01 RR000064-360591/RR/NCRR NIH HHS/ -- M01 RR000064-36S10579/RR/NCRR NIH HHS/ -- M01 RR000064-36S10582/RR/NCRR NIH HHS/ -- M01 RR000064-36S10591/RR/NCRR NIH HHS/ -- M01 RR000064-370579/RR/NCRR NIH HHS/ -- M01 RR000064-370582/RR/NCRR NIH HHS/ -- M01 RR000064-370591/RR/NCRR NIH HHS/ -- M01 RR000064-37S10579/RR/NCRR NIH HHS/ -- M01 RR000064-37S10582/RR/NCRR NIH HHS/ -- M01 RR000064-37S10591/RR/NCRR NIH HHS/ -- M01 RR000064-380579/RR/NCRR NIH HHS/ -- M01 RR000064-380582/RR/NCRR NIH HHS/ -- M01 RR000064-380591/RR/NCRR NIH HHS/ -- M01 RR000064-390579/RR/NCRR NIH HHS/ -- M01 RR000064-390582/RR/NCRR NIH HHS/ -- M01 RR000064-390591/RR/NCRR NIH HHS/ -- M01-RR00064/RR/NCRR NIH HHS/ -- MH061009/MH/NIMH NIH HHS/ -- MH0666730/MH/NIMH NIH HHS/ -- MH64547/MH/NIMH NIH HHS/ -- MH69359/MH/NIMH NIH HHS/ -- NS049261/NS/NINDS NIH HHS/ -- P01 HD035476-03/HD/NICHD NIH HHS/ -- P01 HD035476-04/HD/NICHD NIH HHS/ -- P01 HD035476-04S1/HD/NICHD NIH HHS/ -- P01 HD035476-04S2/HD/NICHD NIH HHS/ -- P01 HD035476-05/HD/NICHD NIH HHS/ -- P50 HD055751/HD/NICHD NIH HHS/ -- P50 HD055751-01/HD/NICHD NIH HHS/ -- P50 HD055751-010002/HD/NICHD NIH HHS/ -- P50 HD055751-019003/HD/NICHD NIH HHS/ -- P50 HD055751-02/HD/NICHD NIH HHS/ -- P50 HD055751-020002/HD/NICHD NIH HHS/ -- P50 HD055751-03/HD/NICHD NIH HHS/ -- P50 HD055751-030002/HD/NICHD NIH HHS/ -- P50 HD055751-04/HD/NICHD NIH HHS/ -- P50 HD055782-01/HD/NICHD NIH HHS/ -- R01 MH057881/MH/NIMH NIH HHS/ -- R01 MH061009/MH/NIMH NIH HHS/ -- R01 MH061009-01A1/MH/NIMH NIH HHS/ -- R01 MH061009-01A1S1/MH/NIMH NIH HHS/ -- R01 MH061009-02/MH/NIMH NIH HHS/ -- R01 MH061009-03/MH/NIMH NIH HHS/ -- R01 MH061009-04A1/MH/NIMH NIH HHS/ -- R01 MH061009-05/MH/NIMH NIH HHS/ -- R01 MH061009-06/MH/NIMH NIH HHS/ -- R01 MH061009-07/MH/NIMH NIH HHS/ -- R01 MH061009-08/MH/NIMH NIH HHS/ -- R01 MH064547/MH/NIMH NIH HHS/ -- R01 MH064547-01/MH/NIMH NIH HHS/ -- R01 MH064547-01S1/MH/NIMH NIH HHS/ -- R01 MH064547-02/MH/NIMH NIH HHS/ -- R01 MH064547-02S1/MH/NIMH NIH HHS/ -- R01 MH064547-03/MH/NIMH NIH HHS/ -- R01 MH064547-04/MH/NIMH NIH HHS/ -- R01 MH064547-05/MH/NIMH NIH HHS/ -- R01 MH069359/MH/NIMH NIH HHS/ -- R01 MH069359-01A2/MH/NIMH NIH HHS/ -- R01 MH069359-02/MH/NIMH NIH HHS/ -- R01 MH069359-03/MH/NIMH NIH HHS/ -- R01 MH069359-04/MH/NIMH NIH HHS/ -- R01 MH069359-05/MH/NIMH NIH HHS/ -- R01 NS049261/NS/NINDS NIH HHS/ -- R01 NS049261-01A2/NS/NINDS NIH HHS/ -- R01 NS049261-02/NS/NINDS NIH HHS/ -- R01 NS049261-03/NS/NINDS NIH HHS/ -- R01 NS049261-04/NS/NINDS NIH HHS/ -- R01 NS049261-05/NS/NINDS NIH HHS/ -- U10 MH066766-02S1/MH/NIMH NIH HHS/ -- U10MH66766-02S1/MH/NIMH NIH HHS/ -- U19 HD035476-06/HD/NICHD NIH HHS/ -- U19 HD035476-07/HD/NICHD NIH HHS/ -- U19 HD035476-08/HD/NICHD NIH HHS/ -- U19 HD035476-09/HD/NICHD NIH HHS/ -- U19 HD035476-10/HD/NICHD NIH HHS/ -- U24 MH081810/MH/NIMH NIH HHS/ -- U24 MH081810-01/MH/NIMH NIH HHS/ -- U24 MH081810-02/MH/NIMH NIH HHS/ -- U24 MH081810-03/MH/NIMH NIH HHS/ -- U24 MH081810-04/MH/NIMH NIH HHS/ -- U54 MH066673/MH/NIMH NIH HHS/ -- U54 MH066673-01A10001/MH/NIMH NIH HHS/ -- U54 MH066673-020001/MH/NIMH NIH HHS/ -- U54 MH066673-030001/MH/NIMH NIH HHS/ -- U54 MH066673-040001/MH/NIMH NIH HHS/ -- U54 MH066673-05/MH/NIMH NIH HHS/ -- U54 MH066673-050001/MH/NIMH NIH HHS/ -- UL1 RR024134/RR/NCRR NIH HHS/ -- UL1 RR024134-03/RR/NCRR NIH HHS/ -- UL1-RR024134-03/RR/NCRR NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2009 May 28;459(7246):569-73. doi: 10.1038/nature07953. Epub 2009 Apr 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19404257" target="_blank"〉PubMed〈/a〉
    Keywords: Autistic Disorder/*genetics ; Case-Control Studies ; Cell Adhesion Molecules, Neuronal/genetics ; Cohort Studies ; Europe/ethnology ; Gene Dosage/*genetics ; Gene Regulatory Networks/genetics ; Genetic Predisposition to Disease/genetics ; Genetic Variation/*genetics ; Genome, Human/*genetics ; Genotype ; Humans ; Neurons/*metabolism ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; Ubiquitin/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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