Wednesday, 17 Jul 2019
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VJPM
Page: 113
Volume 27, Issue 12(197) 2017
Internal validation of the applicability of Recall to independently generated sequence data
Author: Tran Thi Minh Tam and Nguyen Thi Lan Anh
Summary:
The bioinformatics tool (RECall) was developed by British Columbia Centre for Excellence in HIV/AIDS has been tailored specifically for HIV genotyping. The predominant methodology used for HIV genotypic drug resistance testing involves reverse transcriptase PCR (RT-PCR) amplification of extracted viral RNA from plasma followed by population- based sequencing. While the commercially available HIV drug resistance genotyping kits, such as the Trugene (Siemens, Deerfield, IL) and ViroSeq (Abbott Laboratories, Des Plaines, IL) tests, are distributed with custom analysis software; RECall is a software solutions available for genotyping methods developed in-house, for free as a Web application (http://pssm.cfenet.ubc.ca/). Since drug-resistant HIV variants may be present at low frequencies, accurate identification of nucleotide “mixtures” (positions where two or more nucleotides are observed) is required. Differences in individual technicians to identify low-level nucleotide mixtures could result in clinically relevant drug resistance mutations being missed. RECall can be considered as a quality-assessing tool that evaluates the sequencing outputs’ quality. In this report, we validated the applicability of RECall for the automated analysis of HIV drug resistance genotyping to human-verified sequences. Concordance was obtained between human and automated RECall interpretation (99.51% agreement for > 90,000,000 bases compared) and came out with courses of action to deal with sequencing data that improve the quality of testing.
Keywords:
Recall, HIV drug resistant, bioinformatics tool
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13. Tran Thi Minh Tam.pdf
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Happy New Year 2019! Year of the Pig
The Vietnam Journal of Preventive Medicine wish all readers with healthy, happiness and prosperity in the year of the Pig. Happy New Year 2019
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