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
Citations
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SZDB: A Database for Schizophrenia Genetic Research.
TL;DR: It is shown that genes implicated in SZ are highly co-expressed in human brain and proteins encoded by the prioritized SZ risk genes are significantly interacted and the user-friendly SZDB provides high-confidence candidate variants and genes for further functional characterization.
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Germline MC1R status influences somatic mutation burden in melanoma
Carla Daniela Robles-Espinoza,Carla Daniela Robles-Espinoza,Nicola D. Roberts,Shuyang Chen,Finbarr P. Leacy,Finbarr P. Leacy,Ludmil B. Alexandrov,Natapol Pornputtapong,Ruth Halaban,Michael Krauthammer,Rutao Cui,D. Timothy Bishop,David J. Adams +12 more
TL;DR: In melanomas and for somatic C>T mutations, a signature linked to sun exposure, the expected single-nucleotide variant count associated with the presence of an R allele is estimated to be 42% (95% CI, 15–76%) higher than that among persons without an R alleles.
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Targeted next-generation sequencing panel (GlioSeq) provides comprehensive genetic profiling of central nervous system tumors
Marina N. Nikiforova,Abigail I. Wald,Melissa A. Melan,Somak Roy,Shan Zhong,Ronald L. Hamilton,Frank S. Lieberman,Jan Drappatz,Nduka Amankulor,Ian F. Pollack,Yuri E. Nikiforov,Craig Horbinski +11 more
TL;DR: An amplification-based targeted NGS assay that analyzes 30 genes for single nucleotide variants and indels, 24 genes for copy number variations (CNVs), and 14 types of structural alterations in BRAF, EGFR, and FGFR3 genes in a single workflow that allows rapid and cost-effective profiling of brain tumor specimens and thus provides valuable information for patient management.
Journal ArticleDOI
ADCY5-related dyskinesia: Broader spectrum and genotype-phenotype correlations.
Dong Hui Chen,Aurélie Méneret,Jennifer Friedman,Olena Korvatska,Alona Gad,Alona Gad,Emily Bonkowski,Holly A.F. Stessman,Diane Doummar,Cyril Mignot,Mathieu Anheim,Saunder Bernes,Marie Y. Davis,Nathalie Damon-Perrière,Bertrand Degos,David Grabli,David Grabli,David Grabli,Domitille Gras,Fuki M. Hisama,Katherine M. Mackenzie,Phillip D. Swanson,Christine Tranchant,Marie Vidailhet,Marie Vidailhet,Steven Parrish Winesett,Oriane Trouillard,Oriane Trouillard,Laura M. Amendola,Michael O. Dorschner,Michael D. Weiss,Evan E. Eichler,Ali Torkamani,Emmanuel Roze,Emmanuel Roze,Thomas D. Bird,Wendy H. Raskind +36 more
TL;DR: ADCY5-related dyskinesia is a childhood-onset episodic movement disorder with a wide range of hyperkinetic abnormal movements and genotype-specific correlations and mosaicism play important roles in the phenotypic variability.
Journal ArticleDOI
BMP4 loss-of-function mutations in developmental eye disorders including SHORT syndrome
Linda M. Reis,Linda M. Reis,Rebecca C. Tyler,Rebecca C. Tyler,Kala F. Schilter,Kala F. Schilter,Omar A. Abdul-Rahman,Jeffrey W. Innis,Beth A. Kozel,Adele Schneider,Tanya Bardakjian,Edward J. Lose,Donna M. Martin,Ulrich Broeckel,Ulrich Broeckel,Elena V. Semina,Elena V. Semina +16 more
TL;DR: The results significantly expand the number of reported loss-of-function mutations, further support the critical role of BMP4 in ocular development, and provide additional evidence of variable expression/non-penetrance of B MP4 mutations.
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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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.
Journal ArticleDOI
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Amos Marc Bairoch,Rolf Apweiler +1 more
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Journal ArticleDOI
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.