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Showing 1–22 of 22 results
Advanced filters: Author: Ted Sharpe Clear advanced filters

  • Here the authors provide an explanation for 95% of examined predicted loss of function variants found in disease-associated haploinsufficient genes in the Genome Aggregation Database (gnomAD), underscoring the power of the presented analysis to minimize false assignments of disease risk.

    • Sanna Gudmundsson
    • Moriel Singer-Berk
    • Anne O’Donnell-Luria
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-14

  • A large empirical assessment of sequence-resolved structural variants from 14,891 genomes across diverse global populations in the Genome Aggregation Database (gnomAD) provides a reference map for disease-association studies, population genetics, and diagnostic screening.

    • Ryan L. Collins
    • Harrison Brand
    • Michael E. Talkowski
    ResearchOpen Access
    Nature
    Volume: 581, P: 444-451

  • A genomic constraint map for the human genome constructed using data from 76,156 human genomes from the Genome Aggregation Database shows that non-coding constrained regions are enriched for regulatory elements and variants associated with complex diseases and traits.

    • Siwei Chen
    • Laurent C. Francioli
    • Konrad J. Karczewski
    Research
    Nature
    Volume: 625, P: 92-100

  • EGFR mutations are frequent in glioblastoma and lung cancer. Here, the authors perform deep mutational scanning of EGFR, followed by a high-throughput functional screen and analysis of patient data, to identify variants with differing sensitivities to a range of EGFR tyrosine kinase inhibitors.

    • Tikvah K. Hayes
    • Elisa Aquilanti
    • Matthew Meyerson
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-18

  • Samuel Singer and colleagues report an integrative genomic analysis of soft-tissue sarcomas. They survey sequence, copy number and mRNA expression in 207 individuals diagnosed with one of seven major high-grade sarcoma subtypes, and highlight subtype-specific alternations.

    • Jordi Barretina
    • Barry S Taylor
    • Samuel Singer
    Research
    Nature Genetics
    Volume: 42, P: 715-721

  • An analysis of human chromosome 15 — which is altered in Prader-Willi and Angelman syndromes — reveals that it resembles a hall of mirrors, as it contains a number of sequence duplications throughout its length. The evolutionary events that may have led to the high number of duplications was also reconstructed.

    • Michael C. Zody
    • Manuel Garber
    • Chad Nusbaum
    Research
    Nature
    Volume: 440, P: 671-675

  • Genomes and transcriptomes of five distinct lineages of African cichlids, a textbook example of adaptive radiation, have been sequenced and analysed to reveal that many types of molecular changes contributed to rapid evolution, and that standing variation accumulated during periods of relaxed selection may have primed subsequent diversification.

    • David Brawand
    • Catherine E. Wagner
    • Federica Di Palma
    ResearchOpen Access
    Nature
    Volume: 513, P: 375-381

  • Genome sequencing and phylogenomic analysis show that the lungfish, not the coelacanth, is the closest living relative of tetrapods, that coelacanth protein-coding genes are more slowly evolving than those of tetrapods and lungfish, and that the genes and regulatory elements that underwent changes during the vertebrate transition to land reflect adaptation to a new environment.

    • Chris T. Amemiya
    • Jessica Alföldi
    • Kerstin Lindblad-Toh
    ResearchOpen Access
    Nature
    Volume: 496, P: 311-316

  • The genome of the grey short-tailed opossum Monodelphis domestica has been sequenced and analyzed, giving a first peek at a marsupial's genetic code. Of particular interest are the genetics of the immune system, which has been studied as a model for humans, and of the X chromosome for historical reasons.

    • Tarjei S. Mikkelsen
    • Matthew J. Wakefield
    • Kerstin Lindblad-Toh
    Research
    Nature
    Volume: 447, P: 167-177

  • Large-scale loss-of-function screens and TP53 saturation mutagenesis screens in human cancer cell lines suggest that mutational processes combine with phenotypic selection to shape the landscape of somatic mutations at the TP53 locus.

    • Andrew O. Giacomelli
    • Xiaoping Yang
    • William C. Hahn
    Research
    Nature Genetics
    Volume: 50, P: 1381-1387

  • Phytophthora infestans is a fungus-like eukaryote and the most destructive pathogen of potato, with current annual worldwide potato crop losses due to late blight estimated at $6.7 billion. Here, the sequence of the P. infestans genome is reported. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of certain secreted disease effector proteins, probably explaining the rapid adaptability of the pathogen to host plants.

    • Brian J. Haas
    • Sophien Kamoun
    • Chad Nusbaum
    ResearchOpen Access
    Nature
    Volume: 461, P: 393-398

  • Here, the genomes of birds representing eight populations of domestic chickens are compared with the genome of their wild ancestor, the red jungle fowl. The results reveal selective sweeps of favourable alleles and mutations that may have contributed to domestication. One selective sweep, for instance, occurred at the locus encoding the thyroid stimulating hormone receptor, which is important in metabolism and in the timing of vertebrate reproduction.

    • Carl-Johan Rubin
    • Michael C. Zody
    • Leif Andersson
    ResearchOpen Access
    Nature
    Volume: 464, P: 587-591

  • Amit Majithia and colleagues employ a pooled assay in human macrophages to assess the functional effects of all possible missense variants in PPARG. Their study shows the value of saturation mutagenesis and prospective experimental characterization to support diagnostic interpretation of newly discovered missense variants in disease-related genes.

    • Amit R Majithia
    • Ben Tsuda
    • David Altshuler
    Research
    Nature Genetics
    Volume: 48, P: 1570-1575

  • David Jaffe and colleagues report a new algorithm, DISCOVAR, for variant calling and de novo genome assembly. They test the algorithm on a new reference variant call set and demonstrate improved variant calling, particularly in challenging regions of the genome.

    • Neil I Weisenfeld
    • Shuangye Yin
    • David B Jaffe
    Research
    Nature Genetics
    Volume: 46, P: 1350-1355

  • Optic neuritis is an inflammatory optic neuropathy that is frequently—but not always—associated with multiple sclerosis (MS). Despite recent developments in laboratory, imaging and electrophysiological techniques, no consensus guidelines have yet been formulated for the diagnostic work-up in patients presenting with optic neuritis. In this Review, Petzold and colleagues contribute to the development of such a consensus by proposing an investigation protocol for optic neuritis.

    • Axel Petzold
    • Mike P. Wattjes
    • Gordon T. Plant
    Reviews
    Nature Reviews Neurology
    Volume: 10, P: 447-458