scholarly journals ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

2017 ◽  
Author(s):  
Martin Hunt ◽  
Alison E. Mather ◽  
Leonor Sánchez-Busó ◽  
Andrew J. Page ◽  
Julian Parkhill ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
Bacterial Isolate ◽  
Animal Health ◽  
Gram Negative Bacteria ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Gram Negative

AbstractAntimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customisable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods. ARIBA is available at https://github.com/sanger-pathogens/ariba.

scholarly journals Analytical Validation of the Tag-It High-Throughput Microsphere-Based Universal Array Genotyping Platform: Application to the Multiplex Detection of a Panel of Thrombophilia-Associated Single-Nucleotide Polymorphisms

2004 ◽  
Vol 50 (11) ◽  
pp. 2028-2036 ◽  
Author(s):  
Susan Bortolin ◽  
Margot Black ◽  
Hemanshu Modi ◽  
Ihor Boszko ◽  
Daniel Kobler ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Direct Dna Sequencing ◽  
Array Platform ◽  
Genotyping Platform ◽  
Universal Array ◽  
Primer Sets

Abstract Background: We have developed a novel, microsphere-based universal array platform referred to as the Tag-It™ platform. This platform is suitable for high-throughput clinical genotyping applications and was used for multiplex analysis of a panel of thrombophilia-associated single-nucleotide polymorphisms (SNPs). Methods: Genomic DNA from 132 patients was amplified by multiplex PCR using 6 primer sets, followed by multiplex allele-specific primer extension using 12 universally tagged genotyping primers. The products were then sorted on the Tag-It array and detected by use of the Luminex xMAP™ system. Genotypes were also determined by sequencing. Results: Empirical validation of the universal array showed that the highest nonspecific signal was 3.7% of the specific signal. Patient genotypes showed 100% concordance with direct DNA sequencing data for 736 SNP determinations. Conclusions: The Tag-It microsphere-based universal array platform is a highly accurate, multiplexed, high-throughput SNP-detection platform.

scholarly journals Single-Nucleotide Polymorphisms for High-Throughput Genotyping of Anopheles arabiensis in East and Southern Africa

2012 ◽  
Vol 49 (2) ◽  
pp. 307-315 ◽  
Author(s):  
Yoosook Lee ◽  
Stephanie N. Seifert ◽  
Christen M. Fornadel ◽  
Douglas E. Norris ◽  
Gregory C. Lanzaro
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
Southern Africa ◽  
Anopheles Arabiensis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data

2013 ◽  
Vol 29 (18) ◽  
pp. 2245-2252 ◽  
Author(s):  
W.-Y. Yang ◽  
F. Hormozdiari ◽  
Z. Wang ◽  
D. He ◽  
B. Pasaniuc ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Haplotype Inference ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide
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