SIFT: predicting amino acid changes that affect protein function
Pauline C. Ng,Steven Henikoff +1 more
TLDR
SIFT is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study and can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms.Abstract:
Single nucleotide polymorphism (SNP) studies and random mutagenesis projects identify amino acid substitutions in protein-coding regions. Each substitution has the potential to affect protein function. SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study. We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html.read more
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Recent Developments in Genomewide Association Scans: A Workshop Summary and Review
TL;DR: A broad consensus emerged that the time was now ripe for launching genomewide association studies, and several common themes were identified--most notably the considerable efficiency gains of multistage sampling design, specifically those made by testing only a portion of the subjects with a high-densitygenomewide technology, followed by testing additional subjects and/or additional SNPs at regions identified by this initial scan.
Journal ArticleDOI
SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features.
TL;DR: This work has developed a method, SuSPect (Disease-Susceptibility-based SAV Phenotype Prediction), for predicting how likely SAVs are to be associated with disease, which performs significantly better than other available batch methods on the VariBench benchmarking dataset.
Journal ArticleDOI
Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication.
TL;DR: The population history of grapes is estimated and it is confirmed that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness, which solves three ongoing mysteries about plant domestication.
Journal ArticleDOI
Beta-propeller protein-associated neurodegeneration: a new X-linked dominant disorder with brain iron accumulation
Susan J. Hayflick,Michael C. Kruer,Allison Gregory,Tobias B. Haack,Manju A Kurian,Manju A Kurian,Henry Houlden,James C. Anderson,Nathalie Boddaert,Lynn Sanford,Sami I. Harik,Vasuki Dandu,Nardo Nardocci,Giovanna Zorzi,Todd Dunaway,Mark A. Tarnopolsky,Steven Skinner,Kenton R. Holden,Steven J. Frucht,Era Hanspal,Connie Schrander-Stumpel,Cyril Mignot,Delphine Héron,Dawn E. Saunders,Margaret Kaminska,Jean-Pierre Lin,Karine Lascelles,Stephan M. Cuno,Esther Meyer,Barbara Garavaglia,Kailash P. Bhatia,Rajith de Silva,Sarah J. Crisp,Peter Lunt,Martyn Carey,John Hardy,Thomas Meitinger,Holger Prokisch,Penelope Hogarth +38 more
TL;DR: Beta-propeller protein-associated neurodegeneration, the only X-linked disorder of neurodegenersation with brain iron accumulation, is associated with de novo mutations in WDR45 and is recognizable by a unique combination of clinical, natural history and neuroimaging features.
References
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David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
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dbSNP: the NCBI database of genetic variation
Stephen T. Sherry,Minghong Ward,Michael Kholodov,Jonathan Baker,Lon Phan,Elizabeth M. Smigielski,Karl Sirotkin +6 more
TL;DR: The dbSNP database is a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, and is integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data.
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Amos Marc Bairoch,Rolf Apweiler +1 more
TL;DR: The Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT, is described.
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Predicting Deleterious Amino Acid Substitutions
Pauline C. Ng,Steven Henikoff +1 more
TL;DR: A tool that uses sequence homology to predict whether a substitution affects protein function is constructed, which may be used to identify plausible disease candidates among the SNPs that cause missense substitutions.
Journal ArticleDOI
Human non‐synonymous SNPs: server and survey
TL;DR: A World Wide Web server is presented to predict the effect of an nsSNP on protein structure and function and the dependence of selective pressure on the structural and functional properties of proteins is studied.