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  • 1
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    The genomic basis of adaptive evolution in threespine sticklebacks (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-04-07
    Description: Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322419/" 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/PMC3322419/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, Felicity C -- Grabherr, Manfred G -- Chan, Yingguang Frank -- Russell, Pamela -- Mauceli, Evan -- Johnson, Jeremy -- Swofford, Ross -- Pirun, Mono -- Zody, Michael C -- White, Simon -- Birney, Ewan -- Searle, Stephen -- Schmutz, Jeremy -- Grimwood, Jane -- Dickson, Mark C -- Myers, Richard M -- Miller, Craig T -- Summers, Brian R -- Knecht, Anne K -- Brady, Shannon D -- Zhang, Haili -- Pollen, Alex A -- Howes, Timothy -- Amemiya, Chris -- Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team -- Baldwin, Jen -- Bloom, Toby -- Jaffe, David B -- Nicol, Robert -- Wilkinson, Jane -- Lander, Eric S -- Di Palma, Federica -- Lindblad-Toh, Kerstin -- Kingsley, David M -- 095908/Wellcome Trust/United Kingdom -- P50 HG002568/HG/NHGRI NIH HHS/ -- P50 HG002568-09/HG/NHGRI NIH HHS/ -- P50 HG002568-09S1/HG/NHGRI NIH HHS/ -- P50-HG002568/HG/NHGRI NIH HHS/ -- R01 HG003474/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Apr 4;484(7392):55-61. doi: 10.1038/nature10944.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Developmental Biology, Beckman Center B300, Stanford University School of Medicine, Stanford California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22481358" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Alaska ; Animals ; Aquatic Organisms/genetics ; *Biological Evolution ; Chromosome Inversion/genetics ; Chromosomes/genetics ; Conserved Sequence/genetics ; Ecotype ; Female ; Fresh Water ; Genetic Variation/genetics ; Genome/*genetics ; Genomics ; Molecular Sequence Data ; Seawater ; Sequence Analysis, DNA ; Smegmamorpha/*genetics
    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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    Genome sequencing identifies a basis for everolimus sensitivity (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-08-28
    Description: Cancer drugs often induce dramatic responses in a small minority of patients. We used whole-genome sequencing to investigate the genetic basis of a durable remission of metastatic bladder cancer in a patient treated with everolimus, a drug that inhibits the mTOR (mammalian target of rapamycin) signaling pathway. Among the somatic mutations was a loss-of-function mutation in TSC1 (tuberous sclerosis complex 1), a regulator of mTOR pathway activation. Targeted sequencing revealed TSC1 mutations in about 8% of 109 additional bladder cancers examined, and TSC1 mutation correlated with everolimus sensitivity. These results demonstrate the feasibility of using whole-genome sequencing in the clinical setting to identify previously occult biomarkers of drug sensitivity that can aid in the identification of patients most likely to respond to targeted anticancer drugs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633467/" 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/PMC3633467/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Iyer, Gopa -- Hanrahan, Aphrothiti J -- Milowsky, Matthew I -- Al-Ahmadie, Hikmat -- Scott, Sasinya N -- Janakiraman, Manickam -- Pirun, Mono -- Sander, Chris -- Socci, Nicholas D -- Ostrovnaya, Irina -- Viale, Agnes -- Heguy, Adriana -- Peng, Luke -- Chan, Timothy A -- Bochner, Bernard -- Bajorin, Dean F -- Berger, Michael F -- Taylor, Barry S -- Solit, David B -- T32 CA009207/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Oct 12;338(6104):221. doi: 10.1126/science.1226344. Epub 2012 Aug 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22923433" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents/*therapeutic use ; Clinical Trials, Phase II as Topic ; Codon, Nonsense ; Disease-Free Survival ; Drug Resistance, Neoplasm/*genetics ; Everolimus ; Genome, Human ; Genome-Wide Association Study ; Humans ; Molecular Targeted Therapy ; Multiprotein Complexes ; Neoplasm Metastasis ; Neurofibromin 2/genetics ; Proteins/antagonists & inhibitors ; Sequence Deletion ; Sirolimus/*analogs & derivatives/therapeutic use ; TOR Serine-Threonine Kinases ; Tumor Suppressor Proteins/*genetics ; Urinary Bladder Neoplasms/*drug therapy/genetics/pathology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Exome sequencing of lung cancer GEMMs [Genetics] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-10-19
    Description: Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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