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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Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma
Kate Megquier,Jason Turner-Maier,Ross Swofford,Jong Hyuk Kim,Aaron L. Sarver,Chao Wang,Sharadha Sakthikumar,Sharadha Sakthikumar,Jeremy Johnson,Michele Koltookian,Mitzi Lewellen,Milcah C. Scott,Ashley J. Schulte,Luke B. Borst,Noriko Tonomura,Noriko Tonomura,Jessica Alföldi,Corrie A. Painter,Rachael Thomas,Elinor K. Karlsson,Elinor K. Karlsson,Matthew Breen,Jaime F. Modiano,Ingegerd Elvers,Ingegerd Elvers,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh +26 more
TL;DR: Canine hemangiosarcoma closely models the genomic landscape of human angiosarComa of the breast and viscera, and is a powerful tool for investigating the pathogenesis of this devastating disease.
Journal ArticleDOI
PIK3CA Mutations Contribute to Acquired Cetuximab Resistance in Patients with Metastatic Colorectal Cancer.
Jianming Xu,Yan Wang,Youliang Wang,Tao Liu,Ming Ni,Mansheng Li,Li Lin,Fei-jiao Ge,Chun Gong,Jun-Yan Gu,Ru Jia,He-Fei Wang,Yu Ling Chen,Rongrui Liu,Chuanhua Zhao,Zhaoli Tan,Yang Jin,Yunping Zhu,Shuji Ogino,Shuji Ogino,Zhi Rong Qian +20 more
TL;DR: Those with PIK3CA or RAS mutations detected in ctDNA showed a pronounced decrease in progression-free survival than patients with no mutation, which may potentially contribute to acquired cetuximab resistance in patients with mCRC.
Journal ArticleDOI
Vitamin D Related Genes, CYP24A1 and CYP27B1, and Colon Cancer Risk
Linda M. Dong,Linda M. Dong,Cornelia M. Ulrich,Cornelia M. Ulrich,Li Hsu,Li Hsu,David Duggan,Debbie S. Benitez,Emily White,Emily White,Martha L. Slattery,Fred M. Farin,Karen W. Makar,Christopher S. Carlson,Christopher S. Carlson,Bette J. Caan,John D. Potter,John D. Potter,Ulrike Peters,Ulrike Peters +19 more
TL;DR: This is the first study to evaluate these genes in relation to colon cancer, and a possible interaction between CYP27B1 and UV-weighted sun exposure with proximal colon cancer was observed.
Journal ArticleDOI
Spontaneous mutations in the single TTN gene represent high tumor mutation burden.
Ji-Hye Oh,Se Jin Jang,Jihun Kim,Insuk Sohn,Ji-Young Lee,Eun Jeong Cho,Sung-Min Chun,Chang Ohk Sung +7 more
TL;DR: It is suggested that the mutation load within TTN represents high TMB status, and higher than expected TTN mutation frequencies observed in other FLAGS (FrequentLy mutAted GeneS) are associated with late replication time.
Journal ArticleDOI
Nasal Carriage as a Source of agr-Defective Staphylococcus aureus Bacteremia
Davida S. Smyth,Jared M. Kafer,Gregory A. Wasserman,Lili Velickovic,Barun Mathema,Robert S. Holzman,Tiffany A. Knipe,Karsten Becker,Christof von Eiff,Georg Peters,Liang Chen,Barry N. Kreiswirth,Richard P. Novick,Bo Shopsin +13 more
TL;DR: Analysis of 158 paired S. aureus clones from blood and nasal carriage sites in individual patients revealed that recovery of an agr-defective mutant from blood was usually predicted by the agr functionality of carriage isolates, suggesting low correlation between virulence and infectivity.
References
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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
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