The utility and limitation of single nucleotide polymorphism analysis on whole genome amplified mesenchymal tumour DNA in formalin fixed tumour samples

Pathology ◽  
2012 ◽  
Vol 44 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Cher-Wei Liang ◽  
Yow-Shan Lee ◽  
Adrian Marino-Enriquez ◽  
Kochung Tsui ◽  
Shih-Hung Huang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Polymorphism Analysis ◽  
Whole Genome ◽  
Single Nucleotide Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Mesenchymal Tumour ◽  
Single Nucleotide ◽  
Formalin Fixed

scholarly journals Whole-Genome Single-Nucleotide-Polymorphism Analysis for Discrimination of Clostridium botulinum Group I Strains

2014 ◽  
Vol 80 (7) ◽  
pp. 2125-2132 ◽  
Author(s):  
Narjol Gonzalez-Escalona ◽  
Ruth Timme ◽  
Brian H. Raphael ◽  
Donald Zink ◽  
Shashi K. Sharma
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Clostridium Botulinum ◽  
Toxin Gene ◽  
Polymorphism Analysis ◽  
Snp Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type ◽  
Group I

ABSTRACTClostridium botulinumis a genetically diverse Gram-positive bacterium producing extremely potent neurotoxins (botulinum neurotoxins A through G [BoNT/A-G]). The complete genome sequences of three strains harboring only the BoNT/A1 nucleotide sequence are publicly available. Although these strains contain a toxin cluster (HA+OrfX−) associated with hemagglutinin genes, little is known about the genomes of subtype A1 strains (termed HA−OrfX+) that lack hemagglutinin genes in the toxin gene cluster. We sequenced the genomes of three BoNT/A1-producingC. botulinumstrains: two strains with the HA+OrfX−cluster (69A and 32A) and one strain with the HA−OrfX+cluster (CDC297). Whole-genome phylogenic single-nucleotide-polymorphism (SNP) analysis of these strains along with other publicly availableC. botulinumgroup I strains revealed five distinct lineages. Strains 69A and 32A clustered with theC. botulinumtype A1 Hall group, and strain CDC297 clustered with theC. botulinumtype Ba4 strain 657. This study reports the use of whole-genome SNP sequence analysis for discrimination ofC. botulinumgroup I strains and demonstrates the utility of this analysis in quickly differentiatingC. botulinumstrains harboring identical toxin gene subtypes. This analysis further supports previous work showing that strains CDC297 and 657 likely evolved from a common ancestor and independently acquired separate BoNT/A1 toxin gene clusters at distinct genomic locations.

scholarly journals Flow Cytometric Platform for High-Throughput Single Nucleotide Polymorphism Analysis

BioTechniques ◽  
2001 ◽  
Vol 30 (3) ◽  
pp. 661-669 ◽  
Author(s):  
J.D. Taylor ◽  
D. Briley ◽  
Q. Nguyen ◽  
K. Long ◽  
M.A. Iannone ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
High Throughput ◽  
Polymorphism Analysis ◽  
Single Nucleotide Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Flow Cytometric

Single-Nucleotide Polymorphism Analysis by Pyrosequencing

2000 ◽  
Vol 280 (1) ◽  
pp. 103-110 ◽  
Author(s):  
Afshin Ahmadian ◽  
Baback Gharizadeh ◽  
Anna C. Gustafsson ◽  
Fredrik Sterky ◽  
Pål Nyrén ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Polymorphism Analysis ◽  
Single Nucleotide Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide
Sign in / Sign up

Export Citation Format

Share Document