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Gs amplicon variantanalyzer version 3.0 avav3.0 software

Manufactured by Roche
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GS Amplicon VariantAnalyzer version 3.0 (AVAv3.0) is a software application developed by Roche. The core function of AVAv3.0 is to analyze and process genetic sequence data from amplicon-based next-generation sequencing experiments.

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Lab products found in correlation

Gs junior sequencer, by Roche (2 mentions) Thequant it picogreen dsdna reagent, by Thermo Fisher Scientific (2 mentions) Gs junior titanium empcr kit lib a kit, by Roche (2 mentions)

2 protocols using gs amplicon variantanalyzer version 3.0 avav3.0 software

1

Screening for PIK3R2 p.Gly373Arg Mutation

Check if the same lab product or an alternative is used in the 5 most similar protocols
To screen for the recurrent PIK3R2 mutation,
p.Gly373Arg, we performed locus-specific amplification of genomic DNA
followed by GS Junior sequencing. We designed fusion primers containing
genome-specific sequences along with distinct MIDs (multiplex identifier
sequences) used to differentiate samples being run together on the same
plate and sequencing adapters to generate amplicons ranging in size from 290
to 310 bp using primer3plus software. Primer sequences are available upon
request (Dr. Renzo Guerrini). Small DNA fragments were removed using
Agencourt AMPure XP (Beckman Coulter, Beverly, MA) according to the
manufacturer’s protocol. All amplicons were quantified using the
Quant-iT PicoGreen dsDNA reagent (Invitrogen Corporation, Life Technologies,
Carlsbad, CA), pooled at equimolar ratios, amplified by emulsion PCR using
the GS Junior Titanium emPCR kit (Lib-A kit, Roche Applied Science,
Mannheim, Germany) and pyrosequenced in the sense and antisense strands on a
GS Junior sequencer (Roche) following the manufacturer’s
instructions. We performed data analysis using the GS Amplicon Variant
Analyzer version 3.0 (AVAv3.0) software (Roche).
Mirzaa G., Conti V., Timms A.E., Smyser C.D., Ahmed S., Carter M., Barnett S., Hufnagel R.B., Goldstein A., Narumi-Kishimoto Y., Olds C., Collins S., Johnston K., Deleuze J.F., Nitschké P., Friend K., Harris C., Goetsch A., Martin B., Boyle E.A., Parrini E., Mei D., Tattini L., Slavotinek A., Blair E., Barnett C., Shendure J., Chelly J., Dobyns W.B, & Guerrini R. (2015). Characterization of mutations of the phosphoinositide-3-kinase regulatory subunit, PIK3R2, in perisylvian polymicrogyria: a next generation sequencing study. The Lancet. Neurology, 14(12), 1182-1195.
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2

Screening for PIK3R2 p.Gly373Arg Mutation

Check if the same lab product or an alternative is used in the 5 most similar protocols
To screen for the recurrent PIK3R2 mutation,
p.Gly373Arg, we performed locus-specific amplification of genomic DNA
followed by GS Junior sequencing. We designed fusion primers containing
genome-specific sequences along with distinct MIDs (multiplex identifier
sequences) used to differentiate samples being run together on the same
plate and sequencing adapters to generate amplicons ranging in size from 290
to 310 bp using primer3plus software. Primer sequences are available upon
request (Dr. Renzo Guerrini). Small DNA fragments were removed using
Agencourt AMPure XP (Beckman Coulter, Beverly, MA) according to the
manufacturer’s protocol. All amplicons were quantified using the
Quant-iT PicoGreen dsDNA reagent (Invitrogen Corporation, Life Technologies,
Carlsbad, CA), pooled at equimolar ratios, amplified by emulsion PCR using
the GS Junior Titanium emPCR kit (Lib-A kit, Roche Applied Science,
Mannheim, Germany) and pyrosequenced in the sense and antisense strands on a
GS Junior sequencer (Roche) following the manufacturer’s
instructions. We performed data analysis using the GS Amplicon Variant
Analyzer version 3.0 (AVAv3.0) software (Roche).
Mirzaa G., Conti V., Timms A.E., Smyser C.D., Ahmed S., Carter M., Barnett S., Hufnagel R.B., Goldstein A., Narumi-Kishimoto Y., Olds C., Collins S., Johnston K., Deleuze J.F., Nitschké P., Friend K., Harris C., Goetsch A., Martin B., Boyle E.A., Parrini E., Mei D., Tattini L., Slavotinek A., Blair E., Barnett C., Shendure J., Chelly J., Dobyns W.B, & Guerrini R. (2015). Characterization of mutations of the phosphoinositide-3-kinase regulatory subunit, PIK3R2, in perisylvian polymicrogyria: a next generation sequencing study. The Lancet. Neurology, 14(12), 1182-1195.
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