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Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software
Joint Authors
Bignon, Yves-Jean
Poulet, Axel
Privat, Maud
Ponelle, Flora
Viala, Sandrine
Decousus, Stephanie
Perin, Axel
Lafarge, Laurence
Ollier, Marie
El Saghir, Nagi S.
Bidet, Yannick
Uhrhammer, Nancy
Source
Issue
Vol. 2016, Issue 2016 (31 Dec. 2016), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2016-08-30
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
Screening for BRCA mutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data.
However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics.
We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences.
Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of the BRCA genes.
All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing.
Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique.
Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche.
Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers.
As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm) of the BRCA genes, followed by 454 sequencing and AGSA analysis.
AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts.
American Psychological Association (APA)
Poulet, Axel& Privat, Maud& Ponelle, Flora& Viala, Sandrine& Decousus, Stephanie& Perin, Axel…[et al.]. 2016. Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software. BioMed Research International،Vol. 2016, no. 2016, pp.1-11.
https://search.emarefa.net/detail/BIM-1098153
Modern Language Association (MLA)
Poulet, Axel…[et al.]. Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software. BioMed Research International No. 2016 (2016), pp.1-11.
https://search.emarefa.net/detail/BIM-1098153
American Medical Association (AMA)
Poulet, Axel& Privat, Maud& Ponelle, Flora& Viala, Sandrine& Decousus, Stephanie& Perin, Axel…[et al.]. Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software. BioMed Research International. 2016. Vol. 2016, no. 2016, pp.1-11.
https://search.emarefa.net/detail/BIM-1098153
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1098153