scholarly journals Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

10.1186/gm374 ◽  
2012 ◽  
Vol 4 (9) ◽  
pp. 73 ◽  
Author(s):  
Alejandro Sifrim ◽  
Jeroen KJ Van Houdt ◽  
Leon-Charles Tranchevent ◽  
Beata Nowakowska ◽  
Ryo Sakai ◽  
...  
Keyword(s):  
Human Disease ◽  
Nucleotide Variation ◽  
Single Nucleotide Variation ◽  
Single Nucleotide

Sensitive analysis of single nucleotide variation by Cas13d orthologs, EsCas13d and RspCas13d

2021 ◽  
Author(s):  
Xin Qiao ◽  
Yanmin Gao ◽  
Jiaojiao Li ◽  
Zhaoguan Wang ◽  
Hongyan Qiao ◽  
...  
Keyword(s):  
Nucleotide Variation ◽  
Single Nucleotide Variation ◽  
Single Nucleotide ◽  
Sensitive Analysis

Newborn screening and single nucleotide variation profiling of TSHR, TPO, TG and DUOX2 candidate genes for congenital hypothyroidism

2020 ◽  
Vol 47 (10) ◽  
pp. 7467-7475
Author(s):  
Yedukondalu Kollati ◽  
Radha Rama Devi Akella ◽  
Shaik Mohammad Naushad ◽  
Divya Borkar ◽  
Maunika Thalla ◽  
...  
Keyword(s):  
Newborn Screening ◽  
Candidate Genes ◽  
Congenital Hypothyroidism ◽  
Nucleotide Variation ◽  
Single Nucleotide Variation ◽  
Single Nucleotide

Association of Functional Single Nucleotide Variation in the NLRP3 Gene with Survival Outcomes After Unrelated Bone Marrow Transplantation.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3140-3140
Author(s):  
Akiyoshi Takami ◽  
J. Luis Espinoza ◽  
Keitaro Matsuo ◽  
Yasuo Morishima ◽  
Makoto Onizuka ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Conflicts Of Interest ◽  
Nucleotide Variation ◽  
Single Nucleotide Variation ◽  
Single Nucleotide ◽  
Hematopoietic Stem ◽  
Nlrp3 Gene ◽  
Transplant Outcomes ◽  
Functional Relevance ◽  
The Impact

Abstract Abstract 3140 NLRP3 is an intracellular trigger of IL-1β production that plays important roles in the regulation of inflammation and apoptosis. A single nucleotide variation in the 3'-untranslated region of the NLRP3 gene, rs10754558 (+29940G>C), is linked to several immunological diseases. When we examined the impact of the NLRP3 genotype in a cohort consisting of 392 pairs of patients with hematologic malignancies and their unrelated HLA 12/12 matched bone marrow donors transplanted through the Japan Donor Marrow Program, the recipient NLRP3 GG genotype was found to be associated with a significantly worse 5-year overall survival (OS) rate (34% vs. 50%, P=0.006) (Fig. 1) and a trend toward a higher transplant-related mortality (TRM) rate (39% vs. 27%, P=0.09) than the recipient CC or CG genotype. The recipient GG genotype remained statistically significant in the multivariate analysis for OS (hazard ratio [HR], 1.86; 95% confidence interval [CI], 1.22 to 2.22; P=0.004) and TRM (HR, 2.28; 95% CI, 1.20 to 4.35; P=0.01). The donor NLRP3 genotype did not significantly influence the transplant outcomes. Next, we investigated the functional relevance of the NLRP3 +29940G>C variant. When leukocytes from healthy individuals were stimulated in vitro with NLRP3 ligand, the leukocytes with the NLRP3 GG genotype produced significantly more IL-1β than those with the NLRP3 CC or CG genotype (Fig. 2). These findings substantiate the functional relevance of the NLRP3 variant, and suggest that the higher IL-1β secretion in the peri-transplant period by recipients with the NLRP3 GG genotype likely accounts for their poor transplant outcomes. NLRP3 genotyping could therefore be useful in predicting prognoses and creating therapeutic strategies for improving the final outcomes of patients who undergo allogeneic hematopoietic stem cell transplantation. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes

Genomics ◽  
2014 ◽  
Vol 104 (1) ◽  
pp. 1-7 ◽  
Author(s):  
William J. Faison ◽  
Alexandre Rostovtsev ◽  
Eduardo Castro-Nallar ◽  
Keith A. Crandall ◽  
Konstantin Chumakov ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Whole Genome ◽  
Nucleotide Variation ◽  
Single Nucleotide Variation ◽  
Single Nucleotide ◽  
Human Genomes ◽  
Tree Building ◽  
Building Methods

scholarly journals Enzyme-mediated single-nucleotide variation detection at room temperature with high discrimination factor

2015 ◽  
Vol 6 (2) ◽  
pp. 1206-1211 ◽  
Author(s):  
Tongbo Wu ◽  
Xianjin Xiao ◽  
Zhe Zhang ◽  
Meiping Zhao
Keyword(s):  
Room Temperature ◽  
Specific Interaction ◽  
Nucleotide Variation ◽  
Single Nucleotide Variation ◽  
Lambda Exonuclease ◽  
Single Nucleotide ◽  
Chemically Modified ◽  
Modified Dna ◽  
High Discrimination ◽  
Novel Strategy

We present a novel strategy for the highly selective detection of single-nucleotide variation at room temperature, based on an extremely specific interaction between Lambda exonuclease (λ exo) and a chemically modified DNA structure.

Single nucleotide variation in exon 11 of canine BRCA2 in healthy and cancerous mammary tissue

2010 ◽  
Vol 184 (3) ◽  
pp. 351-356 ◽  
Author(s):  
Wei-Li Hsu ◽  
Yi-Hsin Huang ◽  
Tien-Jye Chang ◽  
Min-Liang Wong ◽  
Shih-Chieh Chang
Keyword(s):  
Mammary Tissue ◽  
Nucleotide Variation ◽  
Single Nucleotide Variation ◽  
Single Nucleotide ◽  
Exon 11

scholarly journals Prediction of synonymous corrections by the BE-FF computational tool expands the targeting scope of base editing

2020 ◽  
Author(s):  
Rabinowitz Roy ◽  
Abadi Shiran ◽  
Almog Shiri ◽  
Offen Daniel
Keyword(s):  
Genome Editing ◽  
Point Mutations ◽  
Nucleotide Variation ◽  
Single Nucleotide Variation ◽  
Computational Tool ◽  
Single Nucleotide ◽  
Base Editing ◽  
A Genome ◽  
Wide Range ◽  
Reference Protein

ABSTRACTBase editing is a genome-editing approach that employs the CRISPR/Cas system to precisely install point mutations within the genome. A cytidine or adenosine deaminase enzyme is fused to a deactivated Cas and converts C to T or A to G, respectively. The diversified repertoire of base editors, varied in their Cas and deaminase proteins, provides a wide range of functionality. However, existing base-editors can only induce transition substitutions in a specified region determined by the base editor, thus, they are incompatible for many point mutations. Here, we present BE-FF (Base Editors Functional Finder), a novel computational tool that identifies suitable base editors to correct the translated sequence erred by a given single nucleotide variation. Even if a perfect correction of the single nucleotide variation is not possible, BE-FF detects synonymous corrections to produce the reference protein. To assess the potential of BE-FF, we analysed a database of human pathogenic point mutations and found suitable base editors for 60.9% of the transition mutations. Importantly, 19.4% of them were made possible only by synonymous corrections. Moreover, we detected 298 cases in which pathogenic mutations caused by transversions were potentially repairable by base editing via synonymous corrections, although it had been thought impractical. The BE-FF tool and the database are available at https://www.danioffenlab.com/be-ff.GRAPHICAL ABSTRACT

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