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Typer 4

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Typer 4.0 software is a laboratory tool designed for analyzing and interpreting genetic data. It provides functionalities for DNA typing and sequence analysis. The software is used to process and interpret results from various genetic testing procedures.

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Spelling variants of this product

MassARRAY Typer 4.0 software (25 citations) Sequenom Typer 4.0 Software (25 citations) MassARRAY Typer software version 4.0 (9 citations) MassARRAY Typer version 4.0 (4 citations) TYPER software (version 4.0). (3 citations) Spectro Typer 4.0 software (2 citations) Typer Analyzer 4.0 software (2 citations) MassARRAY Typer software 4.0.3 (2 citations)

112 protocols using typer 4

1

Targeted CpG Methylation Analysis in CACNA1C

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iPLEX assays for six selected CpG sites in CGI 3, located in intron 3 of CACNA1C, were designed using Assay Designer in Typer 4.0 (Sequenom) using bioinformatically bisulfite-converted sequences of the targeted region. Inosine was added to oligonucleotide sequences that contained overlapping CpGs or SNPs. No more than one inosine was allowed in an oligonucleotide to ensure binding specificity. The oligonucleotide sequences for the iPLEX assays are listed in Supplementary Table 3. The amplified products were prepared according to iPLEX manual and dispensed on the same equipment as described above. The data were analyzed in Allelotype mode. Quality control and detection of allele ratios (as a measure of methylation status) were performed using Typer 4.0 (Sequenom). The data were subsequently imported into R (www.r-project.org) for statistical analyses. During all experimental work and QC, the investigator was blinded to affection status. Cases and controls were in addition spread in between each other on each plate during bisulfite conversion and Sequenom analysis to avoid experimental batch effects.
Starnawska A., Demontis D., Pen A., Hedemand A., Nielsen A.L., Staunstrup N.H., Grove J., Als T.D., Jarram A., O'Brien N.L., Mors O., McQuillin A., Børglum A.D, & Nyegaard M. (2016). CACNA1C hypermethylation is associated with bipolar disorder. Translational Psychiatry, 6(6), e831-.
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2

Genotyping Genetic Loci Using Sequenom MassARRAY

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The Sequenom MassARRAY system was used for genotyping genetic loci, and the analysis was performed as follows: 1) PCR amplification of DNA segments containing ANP loci. Purified genomic DNA samples were diluted to specific volumes, and 1 μl of each sample was added to specific wells of a 384-well plate. Next, 4 μl of the PCR amplification system was added, which contained Taq polymerase (1 U), genomic DNA (10 ng), PCR primers (0.1 μmol/l each), and dNTPs (500 μmol/l). PCR was performed at 94°C for 15 min, followed by 45 cycles of 20 s at 94°C, 30 s at 56°C, and 60 s at 72°C with a final extension step of 3 min at 72°C. 2) Shrimp alkaline phosphatase (SAP; 0.5 U) was added to eliminate residual dNTPs, and the reactions were incubated at 37°C for 40 min and then at 85°C for 5 min. 3) The samples were examined after PCR product purification and single base extension, and they were desalted by rinsing. Sample application and spectrometric detection were performed, and the experimental results were analyzed by TYPER 4.0 (Sequenom) to generate genotype data.
Yu Z., Li W., Hou D., Zhou L., Deng Y., Tian M, & Feng X. (2015). Relationship between Adiponectin Gene Polymorphisms and Late-Onset Alzheimer’s Disease. PLoS ONE, 10(4), e0125186.
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3

MALDI-TOF Mass Spectrometry Analysis

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Purified products were placed in a 384-well SpectroCHIP (Sequenom) chip, and the signals were analysed via Matrix-assisted laser desorption/Ionization time of a flight (MALDI-TOF) mass spectrometry; the results were classified with TYPER 4.0 (Sequenom).
Zhao K., Li X., Wang J., Liu J., Gong W., Xu H., Wang J., Jiang L., Dan H., Li J., Zeng X, & Chen Q. (2018). Correlation between prostate stem cell antigen gene expression and oral squamous cell carcinoma. Oncology Letters, 15(6), 9151-9161.
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4

Saliva DNA Genotyping by MALDI-TOF MS

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We designed the primers using Assay Design 3.1 software (Sequenom Inc., San Diego, CA, USA), whose details were presented in Supplementary Table S1.
All consenting participants contributed a 2-mL saliva sample using DNA saliva self-collection tube (Beijing Thinkout Sci-Tech Co., Ltd., Beijing, China). DNA was extracted and purified from all saliva samples via a DNA purification kit (Beijing BioTeke Co., Ltd., Beijing, China). DNA fragments were amplified by the polymerase chain reaction (PCR), whose reaction volume was 5 μL containing 20 ng of genomic DNA template. The PCR product was digested with shrimp alkaline phosphatase (Sequenom Inc., San Diego, CA, USA). Following digestion, the amplified fragment was extended in a 9 μL reaction volume and resolved on a 4% agarose gel. All SNPs were genotyped using the high-throughput genotyping platform, conducted by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS), and the data was collected via the TYPER 4.0 in the MassARRAY System (Sequenom Inc., San Diego, CA, USA). Furthermore, genotyping was repeated in 5% of all samples to verify the accuracy of the results, revealing that the proportion of concordance was greater than 99%.
Chen S., Cai W., Duan S., Gao L., Yang W., Gao Y., Jia C., Zhang H, & Li L. (2021). Association of COMT Polymorphisms with Multiple Physical Activity-Related Injuries among University Students in China. International Journal of Environmental Research and Public Health, 18(20), 10828.
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5

MALDI-TOF-MS Analysis of Purified Samples

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After samples were purified using resin, a MassARRAY Nanod-ispenser (Sequenom, San Diego, CA, USA) was used to transfer the purified products to a SpectroCHIP (Sequenom) chip and MALDI-TOF-MS was used for analysis. We used TYPER 4.0 (Sequenom) to complete the classification and obtain the results.
Chen J., Ma R.L., Guo H., Ding Y.S., Zhang J.Y., Liu J.M., Kerm M., Zhang M., Xu S.Z., Li S.G, & Guo S.X. (2015). Polymorphisms in the PPARγ gene and their association with metabolic syndrome in Uyghurs and Kazakhs from Xinjiang, China. Genetics and molecular research : GMR, 14(2).
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6

Genotyping of GBA and APOE Mutations

Cited 1 time
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The focus of this study was on the most common GBA mutations: N370S and L444P. In addition, we evaluated IVS2+1G>A and V394L. The apolioprotein E4 (ApoE4) was also genotyped as it has known associations with cognitive decline (Harold et al., 2009 (link); Lambert et al., 2009 (link); Verghese et al., 2013 (link)). For those participants who provided consent for genotyping, DNA was extracted from peripheral blood or saliva by standard techniques and screened for SNPs corresponding to IVS2+1G>A, N370S, L444P, and V394L.
PCR and extension primers were designed from sequences containing each target SNP with 100 upstream and downstream bases using Assay Design Suite (a design tool hosted at www.mysequenom.com). Single-base extension reactions were performed on the PCR reactions with the iPlex Gold Kit (Sequenom, San Diego, CA, USA) A Sequenom Compact Mass Array Spectrometer was used to perform (matrix-assisted laser desorption ionization time of flight) mass spectrometry according to the iPlex Gold Application Guide (Sequenom Document #11555, July 22, 2009 version.) The software package Typer 4 (Sequenom) was used to analyze the resulting spectra and the genotype of each SNP/sample was determined from the measured mass of each extended oligo.
Moran E.E., Wang C., Katz M., Ozelius L., Schwartz A., Pavlovic J., Ortega R.A., Lipton R.B., Zimmerman M.E, & Saunders-Pullman R. (2017). Cognitive and motor functioning in elderly glucocerebrosidase mutation carriers. Neurobiology of aging, 58, 239.e1-239.e7.
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7

Targeted Mutation Profiling by Mass Spec

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Briefly, PCR and extension primers for 49 mutations in 23 genes were designed using single base extension based mass spectrometry assay design 3.1 software (supplementary Table S4, available at Annals of Oncology online). Mutation calls were analyzed using Typer 4 (Sequenom, Inc., USA) and were reviewed by manually observing mass spectra.
Chandrani P., Prabhash K., Prasad R., Sethunath V., Ranjan M., Iyer P., Aich J., Dhamne H., Iyer D.N., Upadhyay P., Mohanty B., Chandna P., Kumar R., Joshi A., Noronha V., Patil V., Ramaswamy A., Karpe A., Thorat R., Chaudhari P., Ingle A., Choughule A, & Dutt A. (2016). Drug-sensitive FGFR3 mutations in lung adenocarcinoma. Annals of Oncology, 28(3), 597-603.
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8

Genotyping of SNP Haplotypes in Age-Related Macular Degeneration

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A Sequenom assay was designed to analyze five SNPs that identified the common risk haplotypes on Chr1 (containing the Y402H variant) and Chr10 (near ARMS2/HTRA1). Primers were designed using Sequenom SNP Assay Design software version 3.0 for iPLEX reactions. The protocol and reaction conditions were in accordance with the manufacturer’s instructions. The panel analyzed three SNPs that identified the common Chr1 risk haplotype and two SNPs that identified the common Chr10 risk haplotype (SI Appendix, Table S1); more than one SNP was analyzed for each of these common risk loci to ensure that the genotyping of samples was correct. Genotype identification was performed using the MassARRAY system from Sequenom. The matrix-assisted laser desorption/ionization time-of-flight MS spectra from the Sequenom MassARRAY Analyzer 4 instrument were analyzed using Typer 4.0.20 software (Sequenom). Automated fluorescent cycle DNA sequencing was performed using an Applied Biosystems model 3730 DNA analyzer. STADEN (36 (link)) package Pregap4 1.4b1 software version 1.8b1 (Medical Research Council, Laboratory of Molecular Biology) was used for analysis of sequencing data.
Mcharg S., Booth L., Perveen R., Riba Garcia I., Brace N., Bayatti N., Sergouniotis P.I., Phillips A.M., Day A.J., Black G.C., Clark S.J., Dowsey A.W., Unwin R.D, & Bishop P.N. (2022). Mast cell infiltration of the choroid and protease release are early events in age-related macular degeneration associated with genetic risk at both chromosomes 1q32 and 10q26. Proceedings of the National Academy of Sciences of the United States of America, 119(20), e2118510119.
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9

Genotype Identification via MassARRAY

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Genotype identification was performed with the MassARRAY system from Sequenom. The MALDI-TOF MS spectra from the Sequenom MassARRAY® Analyzer 4 instrument were analyzed using Typer 4.0.20 software (Sequenom, San Diego, USA). Automated fluorescent cycle DNA sequencing66 (link) was performed using an Applied Biosystems model 3730 DNA analyzer. STADEN67 (link) package Pregap4 1.4b1 software Version 1.8b1 (Medical Research Council, Laboratory of Molecular Biology, UK) were used for analysis of sequencing.
Swinkels M., Zhang J.H., Tilakaratna V., Black G., Perveen R., McHarg S., Inforzato A., Day A.J, & Clark S.J. (2018). C-reactive protein and pentraxin-3 binding of factor H-like protein 1 differs from complement factor H: implications for retinal inflammation. Scientific Reports, 8, 1643.
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10

Genotyping of Genetic Variants Associated with Diseases

Cited 4 times
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Five SNPs (rs2320615, rs3792792, rs4958881, rs7708392 and rs10036748) with had minor allele frequency > 5% in the HapMap of the Chinese Han Beijing population that have been reported to be associated with the risk of several diseases and cancers, including systemic lupus erythematosus [16 (link)–18 (link)], systemic sclerosis [21 (link)], asthma [22 (link)], and gastric carcinoma [23 (link)]. They were selected for further genotyping. Primers for the amplification process and single base extension reactions were designed with Sequenom Mass-ARRAY Assay Design 3.0 Software (Sequenom, San Diego, CA, USA). Genotyping of the SNPs was performed with the Sequenom MassARRAY platform [31 ] (Sequenom, San Diego, CA, USA) according to the standard instructions recommended by the manufacturer. Sequenom Typer 4.0 software was used for data management and analyses.
Yue C., Li M., Da C., Meng H., Lv S, & Zhao X. (2017). Association between genetic variants and esophageal cancer risk. Oncotarget, 8(29), 47167-47174.
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