Massarray typer software version 4

Manufactured by Labcorp

Sourced in United States

The MassARRAY Typer software version 4.0 is a nucleic acid analysis tool. It is designed to facilitate the processing and analysis of data generated by the MassARRAY system.

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MassARRAY (137 citations) Typer 4.0 software (112 citations) MassARRAY Typer 4.0 software (25 citations) MassARRAY Typer software (24 citations) TYPER software (15 citations) MassARRAY software (8 citations) MassArray Typer (7 citations) MassARRAY Typer version 4.0 (4 citations) MassARRAY Typer software 4.0.3 (2 citations)

9 protocols using massarray typer software version 4

SNP Genotyping by MassArray

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Genomic DNAs of the participants were extracted from the peripheral blood using TIANamp Blood DNA Kit (Tiangen Biotech, Beijing, China) according to the manufacturer's instructions.
SNP genotyping was performed using the MassArray system (Sequenom, San Diego, CA, USA). The data were analyzed by the MassArray Typer software version 4.0 (Sequenom, San Diego, CA, USA). Assay Designer version 4.0 was used to design primers for multiplexed PCR and single-base extension reactions. Briefly, about 10 ng of genomic DNA was used for genotyping by MassArray iPLEX system at Beijing DNALead Co. Ltd., according to the manufacturer's instructions. The reactions were desalted and transferred to a 384-element SpectroCHIP array. Allele identification was obtained using MALDI-TOF mass spectrometry. The mass spectrograms and genotype data were resolved by the MassArray Typer software version 4.0 (Sequenom).

Qin X.S., Liu J.H., Lyu G.T., Peng M.L., Yang F.N., Qin D.C., Li Y.Z, & Liu Y. (2017). Variants in the Promoter Region of HLA-DQA1 were Associated with Idiopathic Membranous Nephropathy in a Chinese Han Population. Chinese Medical Journal, 130(14), 1677-1682.

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Genomic DNA Extraction and Genotyping

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Blood samples were collected once participants clearly diagnosed and stored at -80°C before DNA extraction. Genomic DNA was extracted from venous blood leukocytes using a genomic extraction kit (Beijing eBios Biotechnology Co., Ltd.), and genotyping was performed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), as previously described [15 ]. Briefly, approximately 30 ng of genomic DNA was used to genotype each sample. The DNA samples were amplified, and the PCR products were used for locus-specific single-base extension reactions. The resulting products were desalted and transferred to a 384 SpectroCHIP array (Sequenom, San Diego, CA, USA). Allele detection was performed using MALDI-TOF-MS. The mass spectrograms were analyzed using MassARRAY Typer software version 4.0 (Sequenom, San Diego, CA, USA). Genotyping was performed on January 2019 and authors had reports of every subject to identify individual participants during or after data collection.

Xu N., Xu H., Zhao M., Xu Y, & Huang L. (2019). Associations of systemic, serum lipid and lipoprotein metabolic pathway gene variations with polypoidal choroidal vasculopathy in China. PLoS ONE, 14(12), e0226763.

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Genotyping Five SNPs in AMD/PCV Genes

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Five single nucleotide polymorphisms (SNPs) in three genes associated with AMD or PCV were selected according to the literature, which were rs10468017 in LIPC[5 (link),6 (link),20 (link)]; rs3764261 in CETP[5 (link),6 (link)]; rs12678919 near LPL[5 (link),6 (link),20 (link)]. We also included LIPC rs1532085 and CETP rs173539, which regulated gene expression and showed impact on HDL levels[21 (link),22 (link)]. Blood samples were collected from all participants and stored at -80°C before DNA extraction. Genomic DNA was extracted from venous blood leukocytes using a genomic extraction kit (Beijing eBios Biotechnology Co., Ltd.), and genotyping was performed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), as previously described [23 (link)]. Briefly, approximately 30 ng of genomic DNA was used to genotype each sample. The DNA samples were amplified, and the PCR products were used for locus-specific single-base extension reactions. The resulting products were desalted and transferred to a 384 SpectroCHIP array. Allele detection was performed using MALDI-TOF-MS. The mass spectrograms were analyzed using MassARRAY Typer software version 4.0 (Sequenom, San Diego, CA, USA).

Meng Q., Huang L., Sun Y., Bai Y., Wang B., Yu W., Zhao M, & Li X. (2015). Effect of High-Density Lipoprotein Metabolic Pathway Gene Variations and Risk Factors on Neovascular Age-Related Macular Degeneration and Polypoidal Choroidal Vasculopathy in China. PLoS ONE, 10(12), e0143924.

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Mass Spectrometry Genotyping Validation

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A total of 12-16 nl of each iPLEX® reaction product were transferred onto a SpectroCHIP® II G96 (SEQUENOM Inc., San Diego, CA, USA) using SEQUENOM® MassARRAY® Nanodispenser (SEQUENOM Inc., San Diego, CA, USA). SpectroCHIP® analysis was carried out by SEQUENOM® MassArray® Analyzer 4 and the SpectroAcquire software Version 4.0 (SEQUENOM Inc., San Diego, CA, USA). Finally data analysis for genotype determination was done using the MassARRAY® Typer software version 4.0 (SEQUENOM Inc., San Diego, CA, USA). In order to confirm the genotypes obtained, randomly selected samples (5 each for case and control cohorts) from each genotype (n = 240) were validated by Sanger Sequencing to ensure accuracy of genotyping results. In all cases, the Sanger Sequencing confirmed the genotyping obtained using MassARRAY.

Chacon-Cortes D., Smith R.A., Haupt L.M., Lea R.A., Youl P.H, & Griffiths L.R. (2015). Genetic association analysis of miRNA SNPs implicates MIR145 in breast cancer susceptibility. BMC Medical Genetics, 16, 107.

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Genotyping of Multiple Myeloma Patients

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The genomic DNA of 739 MM patients and 592 healthy controls was extracted by using a TIANamp Blood DNA Kit (Tiangen Biotech Co., Ltd., Beijing, China) according to the manufacturer's instructions. Primer was designed using the Sequenom MassARRAY Assay Design 4.0 Software for the multiplex polymerase chain reaction (PCR) and for locus-specific single-base extension. PCR was conducted in a 384-well plate, and the products were subjected to locus-specific single-base extension reactions. After desalting, the products were dispensed onto a 384-format SpectroCHIP array (Sequenom), and genotyping was performed by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). The mass spectrograms and genotype data were analysed using MassArray Typer software version 4.0 (Sequenom) 18 (link).

Li B., Liu C., Cheng G., Peng M., Qin X., Liu Y., Li Y, & Qin D. (2019). LRP1B Polymorphisms Are Associated with Multiple Myeloma Risk in a Chinese Han Population. Journal of Cancer, 10(3), 577-582.

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DNA Isolation and Genotyping Protocol

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Genomic DNA was isolated from the whole blood using the blood DNA kit (BioTeKe Corpration, Beijing, China) according to the manufacturer’s protocols. Genotyping was performed with the MassARRAY MALDI-TOF System (Sequenom Inc., San Diego, CA, USA). Primers (forward 5′-ACGTTGGATGAGGTGAAAGGTGATTACTTG-3′ and reverse 5′-ACGTTGGATGGGAAGAGAGAAGGACAAGGG-3′) for polymerase chain reaction or single-base extension were designed using the Assay Designer’s software version 3.0 (Sequenom Inc.) and synthesized by the Beijing Genomics Institute (Beijing, China).
Purified primer extension reaction products were dispensed onto a 384-well Spectro CHIP bioarray using MassARRAY Nanodispenser RS1000 (Sequenom Inc.) and determined by the matrix-assisted laser desorption/ionization time-off light mass spectrometer. Genotype analysis was performed through the MassARRAY Typer software version 4.0 (Sequenom Inc.). Negative controls (without DNA) and duplicate samples were included for quality assurance of genotyping.

Li M., Ma F., Wang J., Li Q., Zhang P., Yuan P., Luo Y., Cai R., Fan Y., Chen S., Li Q, & Xu B. (2018). Genetic polymorphisms of autophagy-related gene 5 (ATG5) rs473543 predict different disease-free survivals of triple-negative breast cancer patients receiving anthracycline- and/or taxane-based adjuvant chemotherapy. Chinese Journal of Cancer, 37, 4.

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Adiponectin Genotyping Protocol

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We selected seven tagSNPs from the adiponectin gene as the study sites; each SNP had a minor allele frequency of more than 5% in the Chinese Han of the Beijing HapMap databank (www.hapmap.org/). Genomic DNA was extracted from whole-blood specimen drawn from each participant using the GOLDMAG Whole Blood Genomic DNA Purification Kit (Golden Magnetic Nano-Biotechnology Co., Ltd. Xi'an, China). PCR primers and single-base extension primers required for SNP genotyping were designed by MassARRAY Assay Design software (version 3.0; Sequenom, San Diego, CA, USA) and synthesised by Shanghai Biological Technology Co., Ltd. (http://www.sangon.com/). The genotyping experiments were performed by Xi'an BaiMei genetic testing centre (http://www.lifegen.com/) with a MassARRAY system based on the matrix-assisted laser desorption ionisation time-of-flight mass spectrometry, according to the manufacturer's instructions. Genotype calling was performed in real-time with the MassARRAY RT software (version 3.1) and analysed with the MassARRAY Typer software version 4.0 (Sequenom).

Chu C., Wang Y., Ren K.Y., Yan D.Y., Guo T.S., Zheng W.L., Yuan Z.Y, & Mu J.J. (2016). Genetic variants in adiponectin and blood pressure responses to dietary sodium or potassium interventions: a family-based association study. Journal of Human Hypertension, 30(9), 563-570.

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Genetic Profiling of Tumor Samples

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AS QIAamp DNA FFPE tissue kit (Qiagen, Hilden, Germany) was used to extract DNA from paraffin-embedded tissue samples, and the presence of tumor cells (>70%) was obtained by trimming the normal and necrotic tissues. Genetic analyses of EGFR, KRAS, and BRAF were performed using the OncoCarta Panel14 (link) (version 1.0; Sequenom, San Diego, CA, USA). Mutation data were analyzed using MassArray Typer software version 4.0 (Sequenom). MET skipping mutation was detected by direct sequencing6 (link) using a PTC-200PCR (Bio-Rad, Hercules, CA, USA) with the forward primer 5’-CTTTGTACGTCTCATGTTAT-3’ and reverse primer 5’-CTCCTAGCGACCTAAC-3’. PCR products were purified and labeled using a BigDye Terminator 3.1 cycle-sequencing kit (Applied Biosystems, Foster City, CA), followed by sequencing in an ABI 3500XL Genetic Analyzer (Applied Biosystems).15 (link)

Wang F., Lu J.B., Wu X.Y., Feng Y.F., Shao Q., An X, & Wang H.Y. (2019). Clinical genetic features and related survival implications in patients with surgically resected large-cell lung cancer. Cancer Management and Research, 11, 5489-5499.

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Genotyping of AMD-Associated SNPs in Koreans

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Patient DNA was obtained from peripheral blood using a DNA extraction kit (QIAamp DNA Maxi kit, Qiagen Inc.). Multiplex polymerase chain reaction using a single base extension technique was performed for SNP genotyping using the iPLEX Gold kit and MassARRAY Typer software version 4.0 (Sequenom, San Diego, CA). Two SNPs known to be major risk alleles for AMD in Koreans, namely CFH rs1061170 and rs800292, were analyzed^{9 (link)}.

Kim K.L., Kim H., Lee Y., Lee C., Joo K., Park S.J., Park K.H., Park S.J, & Woo S.J. (2022). Proteomic genotyping of SNP of Complement Factor H (CFH) Y402H and I62V using multiple reaction monitoring (MRM) assays. Scientific Reports, 12, 19587.

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