Typer software version 4.0

Manufactured by Agena

TYPER software (version 4.0) is a laboratory analysis tool designed for data processing and analysis. The software's core function is to facilitate the interpretation and management of laboratory data.

Automatically generated - may contain errors

Lab products found in correlation

Massarray platform, by Agena (10 mentions) Nanodrop 2000, by Thermo Fisher Scientific (6 mentions) Iplex gold chemistry, by Agena (5 mentions) Bioscience assay design suite version 2, by Agena (3 mentions) Massarray iplex, by Agena (2 mentions) 7500 real time pcr system, by Thermo Fisher Scientific (2 mentions) Massarray nanodispenser, by Agena (1 mentions) Massarray iplex platform, by Agena (1 mentions) Massarray, by Agena (1 mentions) Assay design suite v2, by Agena (1 mentions) Wizard genomic dna purification kit, by Promega (1 mentions) Massarray rs1000, by Agena (1 mentions) Massarray assay design 3, by Agena (1 mentions) Assay design suite version 2.0, by Agena (1 mentions)

16 protocols using typer software version 4.0

STOX1 Genotyping by MassARRAY

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In this study, six SNPs (rs10998449, rs10762244, rs10998461, rs10998468, rs7903209, and rs4472827) in the STOX1 were selected from the DbSNP (

http://www.ncbi.nlm.nih.gov/projects/SNP/

) and 1,000 genome (

http://www.internationalgenome.org/

). All the SNPs were selected at a minor allele frequency >5% in Han Chinese from the 1,000 Genome Projects.
According to the manufacturer's protocol, GoldMag‐Mini Whole Blood Genomic DNA Purification Kit (GoldMag Co. Ltd.) was used to isolate the total genomic DNA from peripheral blood. The Agena Bioscience Assay Design Suite V2.0 software (http://agenacx.com/online-tools) was used to design the extended primer. The MassARRAY Nanodispenser (Agena Bioscience) and MassARRAY iPLEX platform (Agena Bioscience) were used to genotype, and the Agena Bioscience TYPER software (version 4.0) was used to analyze the data. We randomly selected about 10% of the sample to repeat genotyping, and the reproducibility was 100% indicating that our result is reliable.

Yang X., Li F., Xin D., Huang Z., Xue J., Wang B., Da Y., Xing W, & Zhu Y. (2019). Investigation of the STOX1 polymorphism on lumbar disc herniation. Molecular Genetics & Genomic Medicine, 8(1), e1038.

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FNDC1 Genetic Variant Genotyping

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First of all, three variants of FNDC1 (rs420137, rs386360, and rs7763726) were selected from the HapMap database according to the minor allele frequency (MAF) >5% and the unbalanced r² value >0.8. Then, we genotyped them by the Agena MassARRAY platform (Agena Bioscience, San Diego, CA, USA). Finally, the results of genotyping were processed and analyzed by Agena Bioscience Typer software (version 4.0).

He X., Li X., Du X., Han J., Zhang H., Zhu Y, & Ma H. (2022). Rs420137, rs386360 and rs7763726 polymorphisms in fibronectin type III domain containing 1 are associated with susceptibility to coronary heart disease: Analysis in the Han population. Frontiers in Cardiovascular Medicine, 9, 964978.

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IL-1R2 Genetic Variant Genotyping in Peripheral Blood

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We collected 5ml peripheral blood samples from each subject using venipuncture into ethylene diamine tetraacetic acid (EDTA)‐coated blood vacutainer collection tubes and then stored at −80°C for further use. We used the GoldMag‐Mini Whole Blood Genomic DNA Purification Kit (GoldMag. Co. Ltd., Xi'an, China) to extract genomic DNA from blood samples following the manufacturer's instructions. We assessed the purity and concentration of the extracted DNA using a spectrophotometer (NanoDrop 2000; Thermo Fisher Scientific, Waltham, MA) by absorbance measurements at 260 and 280 nm.
Six SNPs (rs11674595, rs4851527, rs719250, rs3218896, rs3218977, and rs2072472) in IL‐1R2 with minor allele frequency (MAF) greater than 0.05 in the global population from the HapMap database and previously reported were adopted for analysis. We used the Agena Bioscience Assay Design Suite V2.0 software (https://agenacx.com/online-tools/) to design the primers of PCR amplification and extension of the six selected SNPs. These SNPs in IL‐1R2 were genotyped in the case and control groups using the Agena MassARRAY platform with iPLEX gold chemistry (Agena Bioscience, San Diego, CA) according to the manufacture's instructions. We used the Agena Bioscience TYPER software (version 4.0) to manage and analyze data.

Wu J., Zhang W., Cai J., Huang S., Niu F., Zhang Y., Bao S, & Jin T. (2019). Influence of IL‐1R2 polymorphisms on endometrial cancer susceptibility in the Chinese Han population. Molecular Genetics & Genomic Medicine, 7(5), e650.

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TagSNP Selection and Genotyping for MIR17HG

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We selected the tagSNPs of MIR17HG with the minor allele frequency (MAF) greater than 0.05 in global population from the 1,000 Genome Projects. As a result, five tagSNPs (rs72640334, rs7336610, rs7318578, rs17735387, and rs1428) were selected using a pairwise Tagger method with r² > 0.8 to capture other SNPs. Primer sequences of amplification and extension for the polymorphisms of MIR17HG were designed using the Agena Bioscience Assay Design Suite V2.0 software (https://agenacx.com/online-tools/). Genotyping was performed with the Agena MassARRAY platform with iPLEX gold chemistry (Agena Bioscience, San Diego, CA) according to the standard protocol recommended by the manufacturer. Data management and analysis were performed using the Agena Bioscience TYPER software, version 4.0.

Chen P., Bai Y., Li Y., Yuan Y., Cheng Y., Pang J., Zhu H, & Chen C. (2019). Association between polymorphisms of MIR17HG and risk of colorectal cancer in the Chinese Han population. Molecular Genetics & Genomic Medicine, 7(6), e667.

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Genotyping LINC-PINT SNPs in Population

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We selected three single nucleotide polymorphisms (SNPs) in LINC-PINT (rs157916, rs16873842, and rs7801029) based on previous research [22 (link), 23 ] The minor allele frequency (MAF) of these SNPs was greater than 5% from the global population in the 1000 Genomes Project (http://asia.ensembl.org/). Additionally, we predicted SNP functions (https://regulomedb.org/regulome-search/). The distribution of SNP genotypes in the control group was consistent with Hardy–Weinberg equilibrium (HWE) (p > 0.05). We utilized ethylene diamine tetraacetic acid (EDTA) tubes to collect peripheral blood samples (5 mL) from each participant. We extracted genomic DNA from whole blood samples using the GoldMag Mini Whole Blood Genomic DNA Purification Kit (GoldMag. Co. Ltd., Xi’an, China) according to the manufacturer’s instructions, and measured DNA concentration and purity using a spectrophotometer (NanoDrop 2000; Thermo Fisher Scientific, Waltham, MA, USA). We genotyped SNPs using Agena MassARRAY (Agena Bioscience, San Diego, CA, USA) as per instructions and operation manual [24 (link)]. The Agena Bioscience TYPER software (version 4.0) was used to manage and analyze genotyping results and ensure that SNP call rates were maintained at over 95%.

Wu Y., Bai M., Yu Y., Wang Y, & Zhang Y. (2023). Association of LINC-PINT polymorphisms with lumbar disc herniation risk among Chinese Han population: a case control study. Journal of Orthopaedic Surgery and Research, 18, 585.

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Genotyping of EYS Gene SNPs

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Five SNPs from EYS were chosen for analysis in this study and they were selected from the GWAS, NCBI dbSNP (http://www.ncbi.nlm.nih.gov/snp) and the 1000 Genomes Project databases (http://www.internationalgenome.org/). All five SNPs had minor allele frequencies >5% in Han Chinese Beijing population. We used the Agena Bioscience Assay Design Suite V2.0 software (https://agenacx.com/online-tools/) to design the primers of PCR amplification and extension of the five selected SNPs. These SNPs in EYS were genotyped in the case and control groups using the Agena MassARRAY platform with iPLEX gold chemistry (Agena Bioscience, San Diego, CA) according to the manufacturer's instructions. We used the Agena Bioscience TYPER software (version 4.0) to manage and analyze data.

Ji D., Xing W., Li F., Huang Z., Zheng W., Hu B., Niu F., Zhu Y, & Yang X. (2019). Correlation of EYS polymorphisms with lumbar disc herniation risk among Han Chinese population. Molecular Genetics & Genomic Medicine, 7(9), e890.

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CLEC16A Variant Genotyping in 1000 Genomes

Cited 1 time

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According to the SNPs data downloaded from the 1000 genome project (http://www.internationalgenome.org/), CLEC16A variants (rs2286973, rs887864, rs12935657, rs11645657 and rs36045143) with minor allele frequencies> 5% and Hardy-Weinberg equilibrium (HWE) > 0.01 were chosen in the global population. According to the specificity principle of primers, these sites meet the requirements. The SNP-related primers (amplification and extension primers) were finished and listed in Supplementary Table S1. 3ml peripheral blood samples were collected from participants in EDTA pretreated tubes. Subsequently, genomic DNA extracted by the GoldMag Whole Blood Genomic DNA Purification Kit (GoldMag Co. Ltd., Xi’an, China), which was used as the PCR amplification template. Subsequently, DNA concentration was estimated by NanoDrop 2000 (Thermo Scientific, Waltham, Massachusetts, United States). Then, using the Agena MassARRAY platform with iPLEX gold chemistry (Agena Bioscience, San Diego, CA, United States), genotyping of CLEC16A variants were proceeded in a 384-well plate. And data management was performed by Agena Bioscience TYPER software, Version 4.0 (Ding et al., 2015 (link)).

Niu Y., Wang H., Li Z., Shamsi B.H., Liu M., Liu J., Wang Q, & Liu Y. (2022). CLEC16A variants conferred a decreased risk to allergic rhinitis in the Chinese population. Frontiers in Genetics, 13, 1053761.

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DNA Extraction and Genotyping Protocol

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Genomic DNA was isolated from 1486 blood samples using the Wizard Genomic DNA Purification Kit (Promega Corporation, WI) in accordance with the manufacturer instructions.^{[22 (link)]} A spectrophotometer was used to measure the purity and concentration of the extracted DNA, and agarose gel electrophoresis was used to determine its quality. The Agena Bioscience Genotyping Tools and MassARRAY Assay Design tools were used to create the primers. Table 1 shows the forward and reverse primers.
TYPER software (version 4.0; Agena Bioscience) and Matrix-assisted laser desorption/ionization-time of flight were used to genotype SNPs.

Liu Y., Wang L., Wang Z, & He S. (2023). Association study of selenium-related gene polymorphisms with geriatric depression in China. Medicine, 102(17), e33594.

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Genotyping of COL6A4P2 Gene SNPs

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Five candidate SNPs in the COL6A4P2 gene were selected with a minor allele frequency (MAF) > 0.05 from the global population in the 1,000 Genome Projects (http://www.internationalgenome.org/). We then used HaploReg v4.1 (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php) to predict the possible functions of the SNPs. The primers for amplification and single-base extension were designed using the Assay Design Suite, V2.0 (https://agenacx.com/online-tools/). Genotyping of the five SNPs was carried out on the MassARRAY iPLEX (Agena Bioscience, San Diego, CA, USA) platform using matrix-assisted laser desorption ionization–time of flight mass spectrometry [17 (link)]. Genotyping results were generated using Agena Bioscience TYPER software, version 4.0. Genotyping was performed by laboratory personnel in a double-blinded manner.

Dang X., Zhao W., Li C., Yang H., Li D., Zhang S, & Jin T. (2021). Impact of COL6A4P2 gene polymorphisms on the risk of lung cancer: A case-control study. PLoS ONE, 16(5), e0252082.

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Genetic Profiling of CARMEN Variants

Cited 3 times

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At least 10 h after fasting, 5 mL of venous peripheral blood samples of participants were collected by professional medical personnel and stored in an EDTA anticoagulation tube and − 80 °C refrigerator. We extracted genomic DNA by using the GoldMag-Mini Whole Blood Genomic DNA Purification Kit (GoldMag Co. Ltd., Xi’an, China). A NanoDrop 2000C spectrophotometer (Thermo Scientifc, Waltham, MA, USA) was applied to detect the DNA concentration and purity. Our present study selected 6 variants located in CARMEN selected from the 1000 Genome Project (https://www.internationalgenome.org/) with minor allele frequencies (MAFs) > 5% in the global population [25 (link)]. Amplification and extension of primers were designed using the Agena MassARRAY Assay Design 3.0 software (Agena, Inc., San Diego, CA, USA). Agena MassARRAY RS1000 (Agena, Inc., San Diego, CA, USA) was used to perform SNP genotyping according to the standard process [16 (link), 25 (link)]. In the end, we completed the data processing with Agena Bioscience TYPER software, version 4.0 [17 (link)].

Guo Y., Cao Y., Gong S., Zhang S., Hou F., Zhang X., Hu J., Yang Z., Yi J., Luo D., Chen X, & Song J. (2020). Correlation analysis between CARMEN variants and alcohol-induced osteonecrosis of the femoral head in the Chinese population. BMC Musculoskeletal Disorders, 21, 547.

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