Taqman genotype software

Manufactured by Thermo Fisher Scientific

Sourced in United States

The TaqMan Genotype software is a bioinformatics tool used for the analysis of genetic data generated from TaqMan genotyping assays. It provides a platform for processing and interpreting the results of TaqMan-based genotyping experiments.

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Lab products found in correlation

Taqman snp genotyping assay, by Thermo Fisher Scientific (3 mentions) Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (2 mentions) Stepone plus real time polymerase chain reaction system, by Thermo Fisher Scientific (2 mentions) Quantstudio real time pcr system, by Thermo Fisher Scientific (1 mentions) Dna blood mini kit, by Qiagen (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions) Taqman assay, by Thermo Fisher Scientific (1 mentions) Real time pcr system, by Thermo Fisher Scientific (1 mentions)

5 protocols using taqman genotype software

Genotyping of liver disease variants

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Genomic DNA extraction from blood samples was performed using a QIAamp (Qiagen, Hilden, Germany) DNA Blood Mini Kit, following the manufacturer’s instructions. To evaluate the extracted DNA qualitatively and quantitatively, we used a Thermo Scientific Nanodrop 2000 spectrophotometer, Wilmington, NC, USA. Each DNA sample underwent genotyping analysis for the variants PNPLA3 rs738409 C>G, TM6SF2 rs58542926 C>T, HSD17B13 rs9992651 G>A, and GCKR rs1260326 T>C. Using TaqMan SNP Genotyping Assays (ThermoFisher, Waltham, MA, USA), the experiment was conducted on a QuantStudio Real-Time PCR System (Applied Biosystems, ThermoFisher, Waltham, MA, USA). TaqMan Genotype Software (Applied Biosystems, QuantStudio^TM Design & Analysis Software v1.4.1) was used to analyze these data for genotype, and allelic discrimination plots were created to show the genotypes of all samples.

Elmansoury N., Megahed A.A., Kamal A., El-Nikhely N., Labane M., Abdelmageed M., Daly A.K, & Wahid A. (2024). Relevance of PNPLA3, TM6SF2, HSD17B13, and GCKR Variants to MASLD Severity in an Egyptian Population. Genes, 15(4), 455.

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Genotyping of RNF213 Polymorphism

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Polymorphisms in the RNF213 gene was determined as previously reported [32 (link)]. Single nucleotide polymorphism (SNP) for rs112735431 (https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=112735431) was analyzed using the TaqMan SNP genotyping assay (Assay ID: C_153120198_10; Applied Biosystems, Foster City, CA, USA) on a StepOnePlus real-time polymerase chain reaction (PCR) system (Applied Biosystems, Foster City, CA, USA). The basic cycling parameters were as follows: hold at 95°C for 10 minutes, followed by 40 cycles of PCR amplification comprising of denaturation at 95°C for 15 seconds, and annealing and extension at 60°C for 1 minute. Genotype calls were evaluated with Applied Biosystems TaqMan Genotype software. The investigators who assessed genotype were blinded to phenotypic information.

Tashiro R., Niizuma K., Khor S.S., Tokunaga K., Fujimura M., Sakata H., Endo H., Inoko H., Ogasawara K, & Tominaga T. (2019). Identification of HLA-DRB1*04:10 allele as risk allele for Japanese moyamoya disease and its association with autoimmune thyroid disease: A case-control study. PLoS ONE, 14(8), e0220858.

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Blood DNA Extraction and SNP Genotyping

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DNA from venous blood was extracted according to standard procedures. Single-nucleotide polymorphisms (SNPs) were genotyped using an Open Array Real-Time PCR System Instrument (Applied Biosystems, Foster City, California, USA). Allelic discrimination was performed using TaqMan Genotype Software (Applied Biosystems). Genotyping success rates for the SNPs were between 85 and 98%.

Hukic D.S., Ösby U., Olsson E., Hilding A., Östenson C.G., Gu H.F., Ehrenborg E., Edman G., Schalling M., Lavebratt C, & Frisén L. (2017). Genetic variants of increased waist circumference in psychosis. Psychiatric Genetics, 27(6), 210-218.

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Genotyping SNP rs112735431 in RNF213 Gene

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Single nucleotide polymorphism (SNP) c.14576G>A (rs112735431) in the RNF213 gene (https://www.ncbi.nlm. nih.gov/projects/SNP/snp_ref.cgi?rs=112735431) was determined, as described previously. [31] [32] [33] Briefly, DNA was extracted from saliva or blood samples using the QIAamp DNA Mini Kit (QIAGEN) according to the manufacturer's instructions. SNP rs112735431 in the RNF213 gene was analyzed by the TaqMan SNP genotyping assay (Assay ID: C_153120198_10; Applied Biosystems) on a StepOne-Plus real-time polymerase chain reaction system (Applied Biosystems). The basic cycling parameters were as follows: primary denaturation at 95°C for 10 minutes, followed by 40 cycles of denaturation at 95°C for 15 seconds, and annealing and extension at 60°C for 1 minute. Genotype signals were assessed using Applied Biosystems TaqMan Genotype software by the investigators while blinded to phenotypic information.

Tashiro R., Fujimura M., Katsuki M., Nishizawa T., Tomata Y., Niizuma K, & Tominaga T. (2021). Prolonged/delayed cerebral hyperperfusion in adult patients with moyamoya disease with RNF213 gene polymorphism c.14576G>A (rs112735431) after superficial temporal artery-middle cerebral artery anastomosis. Journal of neurosurgery, 135(2).

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Genotyping of PADI2 and PADI4 SNPs

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Genomic DNA was isolated by standard techniques from a blood sample collected in tubes with EDTA as an anticoagulant. The SNPs were genotyped through allele discrimination assay using commercial TaqMan assays (Applied Biosystems, San Francisco, CA, USA). The evaluated PADI2 SNPs were C_2190445_20 (rs1005753/Intron, cat. 4351379) and C_2190476_1_ (rs2235926/3′UTR, Cat.4351379). The evaluated PADI4 SNPs were C_22275072_10 (rs11203366/Intron, cat: 4351379), C_22275081_10 (rs11203367/Intron, cat:4351379), and C_2995365_20 (rs874881/5′UTR, cat:4351379). We used quantitative polymerase chain reaction (qPCR) according to the supplier's instructions [StepOnePlus™, Applied Biosystems, Carlsbad, CA, USA]. The thermal cycling settings were: denaturation at 60 °C for 30 s, followed by 40 cycles of 95 °C for 10 min and 95 °C for 15-sec alignment and extension at 60 °C 1 min and 4 °C. Genotype analysis was performed using TaqMan Genotype software (Applied Biosystems™ Real-Time PCR system, USA). We extracted information on the frequency of each SNP in other populations from the ALFA project for comparison with our results.

Gutiérrez-Pérez I.A., Buendía-Roldán I., Zaragoza-García O., Pérez-Rubio G., Villafan-Bernal J.R., Chávez-Galán L., Parra-Rojas I., Hernández-Zenteno R.D., Fricke-Galindo I., Castro-Alarcón N., Bautista-Becerril B., Falfán-Valencia R, & Guzmán-Guzmán I.P. (2024). Association of PADI2 and PADI4 polymorphisms in COVID-19 host severity and non-survival. Heliyon, 10(6), e27997.

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