The largest database of trusted experimental protocols

Typer software version 4

Manufactured by Agena
Sourced in United States

Typer software version 4.0.26.74 is a lab equipment product designed for data analysis and processing. The software provides core functionalities for handling and manipulating data, without extrapolation on intended use.

Automatically generated - may contain errors

5 protocols using typer software version 4

1

Comprehensive Pharmacogenetic Panel Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
The comprehensive pharmacogenetic panel uses multiplex polymerase chain reaction (PCR) and single base extension (SBE) using the Agena SpectroCHIP II and MassARRAY Analyzer 4 platform, as per manufacturer instructions (Agena Biosciences, San Diego, CA). In brief, for each sample 10–20 ng of genomic DNA was amplified in six independent 5 µl multiplex PCR reactions, which consisted of an initial denaturation step at 95°C for 2 minutes followed by 45 cycles (95°C for 30 seconds, 60°C for 30 seconds, and 72°C for 2 minutes). Amplicons were inactivated by shrimp alkaline phosphatase (Agena Biosciences, San Diego, CA) and subjected to six corresponding multiplex SBE reactions using 2 µl of SBE reagent (Agena Biosciences), which consisted of an initial denaturation step at 95°C for 30 seconds followed by 40 cycles (95°C for 5 seconds (52°C for 5 seconds and 80°C for 5 seconds) × 5). SBE products were conditioned with resin to remove salts, spotted on a SpectroCHIP II array, and read on the MassARRAY Analyzer 4 system. Genotypes at all targeted loci were determined by SBE peak intensity and Typer software version 4.1 (Agena Biosciences, San Diego, CA), and diplotypes for selected genes were inferred by a haplotype translation table and Typer software version 4.1.
+ Open protocol
+ Expand
2

Targeted cfDNA Genotyping Using MassARRAY

Check if the same lab product or an alternative is used in the 5 most similar protocols
PCR was performed using 10 ng cfDNA per plex according to manufacturer's instructions (Agena Bioscience, San Diego, CA). Reactions were incubated initially at 94°C for 4 min. Forty-five cycles of PCR were performed at 94°C for 30 s, 56°C for 30 s, and 72°C for 1min. The PCR was completed with a final incubation of 5 minutes at 72°C. Thermocyling and incubation were performed in a GeneAmp PCR System 9700 (Thermo Fisher Scientific). Amplified products (5mL) were treated with shrimp alkaline phosphatase for 40 minutes at 37°C, followed by denaturation for 10 minutes at 85°C. Single-base extension was performed at 94°C for 30 s, followed by 40 cycles at 94°C for 5 s with five nested cycles of 52°C for 5 s, then 80°C for 5 s and incubation at 72°C for 3 min. Streptavidin-coated magnetic beads were used to capture the amplicon. Beads with captured products were pelleted using a magnet and, suspended with 13mL of elution solution, and incubated at 95°C for 5 minutes. Eluted products were conditioned with 5 mL (3 mg) of anion exchange resin slurry. Finally, the analyte was dispensed onto a Spectro CHIPArray solid support using a MassARRAY RS1000 Nano-dispenser. Data were acquired via matrix-assisted laser desorption/ionization time-of-flightmass spectrometry using the MassARRAY Analyzer. Data analysis were performed using Typer software version 4.0.26.74 (Agena Bioscience)
+ Open protocol
+ Expand
3

Quantitative Mutant Allele Detection

Check if the same lab product or an alternative is used in the 5 most similar protocols
Data were analysed with the Typer software version 4.0.26.74 (Agena Bioscience, San Diego, CA, USA). The signal intensity for the mutant allele was normalized to the capture control peaks. An intensity value = 1 indicates that the peak intensity in the mutant allele is equal to the peak intensity of the average of the five capture control peaks. The capture control peaks are biotin-labelled, non-reactive oligonucleotides that are added to the extension reaction and used as an internal control for the streptavidin-bead capture and elution of the mutant extension product steps. Mutant allele calls were returned by an automated software report specific for the UltraSEEK™ Lung Panel. A signal-to-noise ratio ≥6 and a z-score ≥7 were considered significant. For allele calling, the reporter algorithm considered the instrument-specific baseline for each mutation assay. The assay-specific noise was assessed by analysing a cohort of wild-type samples and the mutant call significance was controlled by analysing commercial mutation controls as titration of the mutant allele frequencies down to the limit of detection of 0.1%.
+ Open protocol
+ Expand
4

Mutation Detection Using Typer Software

Check if the same lab product or an alternative is used in the 5 most similar protocols
Data analysis was performed using Typer software version 4.0.26.74 (Agena Bioscience). The software acquired raw peak intensity data for all assay products, and a linear least squares function was used to fit intensities of the capture control assays and determine the per-well data quality and the normalization factor. The intensity of each assay was normalized to the linear fit of the internal controls. Mutations were detected using robust Z-score (median absolute deviationebased Z-score). A robust Z-score was calculated for each assay using the median and the median absolute deviation values previously established for known wild-type samples. These data served as the historical baseline for the mutation detection and were used within each data analysis. Samples that exceeded the user-defined assay Z-score cutoff (default of 10) and met the peak quality criteria (adjustable minimum peak intensity and call probability of 0.8 or better) were labeled as containing the mutation by the analysis software and reported accordingly.
+ Open protocol
+ Expand
5

Single-Base Extension Genotyping Workflow

Check if the same lab product or an alternative is used in the 5 most similar protocols
The single-base extension (SBE) reaction was performed with the iPLEX Pro Reagent kit (Agena Bioscience, Inc.) in a total reaction volume of 9 μL. For the SBE reaction, 0.619 μL H2O, 0.2 μL terminator mix, 0.2 μL iPLEX Pro buffer, 0.94 μL extension probe cocktail, and 0.041 μL ThermoSequenase enzyme were mixed with the products of SAP treatment, using the thermocycling conditions: 94°C for 30 s; 40 cycles at 94°C for 5 s with 5 cycles of 52°C for 5 s and 80°C for 5 s; and a final 72°C for 3 mins. During the SBE reaction, the probe is extended by one mass-modified nucleotide depending on the nucleotide position of interest. The products of the SBE reaction were desalted by rotation with a cationic ion exchange resin (Agena Bioscience, Inc.) for 60 mins. The purified product was spotted onto a 384-spot SpectroChip II (Agena Bioscience, Inc.) using the Nanodispenser RS 1000 equipment (Agena Bioscience, Inc.) and then scanned using the mass spectrometry of MassARRAY system. The results were analyzed by Typer software version 4.1 (Agena Bioscience, Inc.).
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!