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Massarray typer software v4

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The MassARRAY Typer software v4.0 is a core software component used for the analysis of genetic data generated from the MassARRAY system. The software enables users to process, analyze, and interpret the results of genetic assays performed on the MassARRAY platform.

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Lab products found in correlation

Massarray system, by Agena (2 mentions) Coreexome 24, by Illumina (1 mentions) Assay design suite v2, by Agena (1 mentions) Spectrochiparrays, by Agena (1 mentions) Applied biosystems geneamp pcr system 9700, by Thermo Fisher Scientific (1 mentions) Massarray 4 system, by Agena (1 mentions) Shrimp alkaline phosphatase, by Agena (1 mentions) Spectrochip, by Agena (1 mentions) Massarray iplex system, by Agena (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions)

5 protocols using massarray typer software v4

1

Genotyping Histone Modification Genes in EPF

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Genotype data were available from a previous study using microarray hybridization (CoreExome-24, version 1.1, Illumina, San Diego, CA, USA) [19 (link)]. The genomic positions of 144 genes, encoding HATs (12) and HDACs (18) and members of histone acetylation (59) and deacetylation (55) complexes, were identified, considering 1000 base pairs downstream and upstream from the sequence for the longest transcript, according to the human genome version GRC37/hg19 (NCBI gene) [20 (link)] (Table S1). A total of 2486 SNPs located in these gene sequences were extracted from DNA microarray data of EPF samples.
SNPs associated with EPF were genotyped in the SPF samples using the iPLEX platform of the MassARRAY system (Agena Bioscience, San Diego, CA, USA). The primer sequences are available in Table S2. MassARRAY Typer software (v4.0) (Agena Bioscience, San Diego, CA, USA) with standard settings was used to call the genotypes. The genotype distribution followed the Hardy–Weinberg equilibrium in patients, controls, and the set of participants (data not shown), except for rs13339618 (pcontrols = 0.049; pall participants = 0.005).
Sulzbach Denardin M., Bumiller-Bini Hoch V., Salviano-Silva A., Lobo-Alves S.C., Adelman Cipolla G., Malheiros D., Augusto D.G., Wittig M., Franke A., Pföhler C., Worm M., van Beek N., Goebeler M., Sárdy M., Ibrahim S., Busch H., Schmidt E., Hundt J.E., Petzl-Erler M.L, & Beate Winter Boldt A. (2023). Genetic Association and Differential RNA Expression of Histone (De)Acetylation-Related Genes in Pemphigus Foliaceus—A Possible Epigenetic Effect in the Autoimmune Response. Life, 14(1), 60.
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2

Mass Spectrometry Genotyping Protocol

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Mass spectrometry genotyping was performed using the MassARRAY system (Agena Bioscience, USA) when the variant was not validated by Sanger sequencing. Single‐plex assay was designed by Assay Design Suite v2.0 (Agena Bioscience, USA) and synthesized by BGI (Table S2). According to standard procedures, 1 μl genomic DNA was required in each 5 μl PCR reaction mix. The data were collected by MassARRAY Typer software v4.0 (Agena Bioscience, USA). For quality control, a negative control without genomic DNA and a positive control using normal genomic DNA as PCR template were undertaken simultaneously with clinical samples. The normal genomic DNA was taken from a healthy Han Chinese with known genome data at database (http://yh.genomics.org.cn/index.jsp).
Zheng J., Zhang H., Banerjee S., Li Y., Zhou J., Yang Q., Tan X., Han P., Fu Q., Cui X., Yuan Y., Zhang M., Shen R., Song H., Zhang X., Zhao L., Peng Z., Wang W, & Yin Y. (2019). A comprehensive assessment of Next‐Generation Sequencing variants validation using a secondary technology. Molecular Genetics & Genomic Medicine, 7(7), e00748.
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3

SNP Genotyping for Sample Identification

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DNA samples were normalized to 5–10 ng/μl, and identity test was performed using iPLEX® Pro Sample ID Panel kit (Cat. No. 25094, Agena Bioscience, San Diego, CA). Multiplex-PCR targeting 44 identity SNPs was carried out in a 5-μl volume on an Applied Biosystems GeneAmp® PCR System 9700 (Thermo Fisher Scientific, Waltham, MA) with the cycling program recommended by the manufacturer’s manual. After PCR, amplicons were treated with 5 U shrimp alkaline phosphatase (SAP; Agena Bioscience, San Diego, CA USA) and followed by adding 2 μl single-base extension (SBE) cocktail (Agena Bioscience, San Diego, CA) to continue the SBE reaction on a GeneAmp® PCR System 9700 with the cycling program recommended by the manufacturer. SBE products were cleaned up using an ion-exchange resin and then spotted on SpectroCHIP arrays (Agena Bioscience, San Diego, CA USA). Raw data were acquired on a MassARRAY® 4 system (Agena Bioscience, San Diego, CA USA) by Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis. Genotypes for 44 SNPs were generated by MassARRAY Typer software v4.0 (Agena Bioscience, San Diego, CA).
Manheimer K.B., Richter F., Edelmann L.J., D’Souza S.L., Shi L., Shen Y., Homsy J., Boskovski M.T., Tai A.C., Gorham J., Yasso C., Goldmuntz E., Brueckner M., Lifton R.P., Chung W.K., Seidman C.E., Seidman J.G, & Gelb B.D. (2018). Robust identification of mosaic variants in congenital heart disease. Human genetics, 137(2), 183-193.
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4

Genotype Detection Using SpectroCHIP

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Prior to each run, the extension products were spotted on to the SpectroCHIP® (Agena) using the Agena MassARRAY® Nanodispenser (Agena), which was immediately loaded into the Agena MassARRAY® Analyser 4 for genotype detection of each SNP in the assay by the SpectroAcquire v4.0 software (Agena). Final data analysis was performed using the MassARRAY® Typer software v4.0 (Agena).
Bradshaw G., Haupt L.M., Aquino E.M., Lea R.A., Sutherland H.G, & Griffiths L.R. (2019). Single Nucleotide Polymorphisms in MIR143 Contribute to Protection against Non-Hodgkin Lymphoma (NHL) in Caucasian Populations. Genes, 10(3), 185.
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5

SNP Genotyping of Peripheral Blood DNA

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Genomic DNA was extracted from peripheral blood of participants using QIAamp DNA mini kit (Qiagen, German). SNP genotyping was carried out by the MassArray iPLEX system (Agena, USA) at Beijing DNALead Co. LTD. All procedures were performed according to the manufacturer’s instructions. Ten nanograms of genomic DNA was amplified by multiplex PCR and then the amplicons were subjected to locus-specific single-base extension reactions. The extended products were desalted and transferred to a 384-element SpectroCHIP array. Allele detection was performed using MALDI-TOF mass spectrometry, and the MassArray TYPER software v4.0 (Agena, USA) was applied to analyze the mass spectrograms and assign genotype. Afterwards, we eliminated the subjects with call rate less than 80%, and the remaining subjects were further analyzed.
Qin X., Wang C., Lu G., Peng M., Cheng G., Zhu H., Cao Y., Liu J., Li Y., Cai H., Yang F., Liu Y., Chen X., Li L., Wan N., Wen X., Li S., Nie R., Qin D., Li Y, & Liu Y. (2017). Risk alleles for IgA nephropathy-associated SNPs conferred completely opposite effects to idiopathic membranous nephropathy in Chinese Han. Immunologic Research, 65(5), 1059-1064.
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