Massarray typer 4

Manufactured by Labcorp

Sourced in United States

The MassARRAY Typer 4.0 software is a product developed by Labcorp. It is a software application used for the analysis and interpretation of data generated from the MassARRAY system, a mass spectrometry-based genotyping platform.

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25 protocols using massarray typer 4

Genotyping of Genetic Variants Using MALDI-TOF Mass Spectrometry

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Genomic DNA was isolated from peripheral blood using standard protocols for genetic analysis40 (link). Variants genotyping was done using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry by Bioyong Technologies (Beijing, China) following manufacturers’ instructions14 (link)47 (link). Locus-specific amplifying primers, and single-base extending primers, were designed using Sequenom Assay Design 3.1 software, and were synthesized and diluted as required. Primer quality was assayed using a mass spectrometric system42 (link)48 (link). Locus-specific amplification by multiplex PCR, and purification of PCR products, were conducted as previously described14 (link)47 (link)49 (link). MassARRAY Typer 4.0 software (Sequenom) was used to analyze spectrometric results and generate the genotype data of each variant50 (link). All the procedures were performed by investigators blinded to sample status, i.e., from case or control subjects. Duplicate samples, positive and negative controls, were included to confirm genotyping accuracy. Direct sequencing of the amplicons containing these variants in 8% of randomly selected samples was carried out as quality controls to test the reliability51 (link)52 (link).

Yuan L., Song Z., Deng X., Zheng W., Guo Y., Yang Z, & Deng H. (2016). Systematic analysis of genetic variants in Han Chinese patients with sporadic Parkinson’s disease. Scientific Reports, 6, 33850.

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Genotyping of MIR137 and ZNF804A

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We extracted genomic DNA from whole blood using the EZgene Blood gDNA Miniprep Kit (Biomiga, San Diego, CA). MIR137 rs1625579 and ZNF804A rs1344706 were then genotyped using the iPLEX Gold Assay (Sequenom, San Diego, CA), following the manufacturer's instructions and using primers (Supplementary Table 1), and designed using Sequenom Assay Design 3.1 software. The accuracy of genotyping was assessed by analyzing every sample in duplicate. Alleles were automatically called with Sequenom's MassARRAY Typer 4.0 software and verified by two independent reviewers. Three subjects with missing genotype data were excluded from further analysis. MIR137 GG genotypes were not identified in our current population. The reference frequency of rs1625579 in dbSNP database (http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1625579) supports this phenomenon.

Liu B., Zhang X., Hou B., Li J., Qiu C., Qin W., Yu C, & Jiang T. (2014). The Impact of MIR137 on Dorsolateral Prefrontal–Hippocampal Functional Connectivity in Healthy Subjects. Neuropsychopharmacology, 39(9), 2153-2160.

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SNP Genotyping using Sequenom MassARRAY

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Each DNA sample was diluted to working concentrations of 50ng/μl for genotyping. Assay design and SNP genotyping were performed by CapitalBio (Beijing, China) using the Sequenom MassARRAY platform (Sequenom, San Diego, CA). Primers were designed by Genotyping Tools and MassARRAY Assay Design software (version 3.0, Sequenom Inc., San Diego, California). SNPs were genotyped using the Sequenom MassARRAY iPLEX platform. Data was processed and analyzed by Sequenom MassArray TYPER 4.0 software.

Wang C., Nie H., Li Y., Liu G., Wang X., Xing S., Zhang L., Chen X., Chen Y, & Li Y. (2016). The study of the relation of DNA repair pathway genes SNPs and the sensitivity to radiotherapy and chemotherapy of NSCLC. Scientific Reports, 6, 26526.

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Genotyping SNPs from Blood DNA

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Genomic DNA was extracted from peripheral blood. All of the obtained DNA samples were stored at −80°C. All the primers were designed by MassArray Assay Design 3.1 (Sequenom Inc., San Diego, CA, USA). SNPs were geno-typed via the Sequenom MassArray system (BioMiao Biotechnology (Beijing) Co. Ltd) and analyzed with the MassArray Typer 4.0 software (Sequenom).9

Li M., Wang W., Zhang L., Xin W., Zhao Y., Huan L., Yu J., Zhang H., Zhang J., Yang S., Liang D., Yang W, & Yang X. (2019). Genetic polymorphisms in Sox17 associated with intracranial aneurysm in Chinese Han people: a genotype-phenotype study. Neuropsychiatric Disease and Treatment, 15, 779-783.

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Genotyping of ERCC2 rs13181 SNP

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The rs13181 SNP in the ERCC2 gene was genotyped by BGI (Beijing, China) as described15 (link) using allele-specific, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Primers designed using MassARRAY Assay Design 3.1 software (Sequenom, San Diego, CA, USA) were used to amplify fragments spanning the rs13181SNP in a 384-well ABI Veriti PCR System (Applied Biosystems, Foster City, CA, USA) in accordance with the manufacturer’s instructions. Amplification reactions (5 μL) consisted of 1 μL DNA (20 ng/μL) and 4 μL Master Mix, and reaction conditions were as follows: 94°C for 5 min, then 45 cycles of 94°C for 20 sec and 56°C for 30 sec, followed by 72°C for 1 min. Genotypes at rs13181 were analyzed using MassARRAY TYPER 4.0 software (Sequenom). Rates of successful genotyping were 99.8% (439/440) among the NPC patients and 100% (431/431) in controls.

Wei Z., Yao M., Ning S., Wu Y., Zhou X., Zhong C., Yan K, & Xie Y. (2021). The Association of Single-Nucleotide Polymorphism rs13181 in ERCC2 with Risk and Prognosis of Nasopharyngeal Carcinoma in an Endemic Chinese Population. Pharmacogenomics and Personalized Medicine, 14, 359-367.

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Genotyping of DC-SIGN SNPs by MALDI-TOF

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The DC-SIGN SNPs rs7252229, rs4804803, rs2287886, and rs735240 were genotyped in all subjects as described [17 (link)] using allele-specific matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, with support from BGI (Beijing, China). Fragments spanning the SNPs were amplified by PCR using primers designed with MassARRAY Assay Design 3.1 Software (Sequenom, San Diego, CA, USA). Amplifications were conducted in a 384-well ABI Veriti PCR System (Applied Biosystems) following the manufacturer's instructions. Amplification reactions (5 μL) contained 4 μL Master Mix and 1 μL DNA (20 ng/μL), and reaction conditions were as follows: 94°C for 5 min, followed by 45 cycles of 94°C for 20 sec, 56°C for 30 sec, and 72°C for 1 min. Alleles were analyzed using MassARRAY TYPER 4.0 software (Sequenom). Successful genotyping rates were 99.8% (560/561) in the control group for rs7252229, rs4804803, and rs735240, respectively, and were 99.8% (476/477) in the NPC group and 99.6% (559/561) in the control group for rs2287886.

Li S., Lu Z., Yao M., Ning S., Wu Y., Zhou X., Zhong C., Yan K., Xie Y, & Wei Z. (2017). Association of Single-Nucleotide Polymorphisms in DC-SIGN with Nasopharyngeal Carcinoma Susceptibility. Disease Markers, 2017, 6309754.

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Multiplex SNP Genotyping Using Sequenom

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Sequence-tagged sites containing SNP information developed⁴⁶ (link) were used as queries in blastn searches against Glyma1.01 with default parameters. Multiplex assays for 1,000 randomly selected SNPs distributed throughout the genome (Supplementary Table S3) were designed to amplify low-copy sequences in Sequenom Assay Design 3.1 software (Sequenom). The Sequenom MassARRAY system⁴⁷ (link) was used for SNP genotyping. Multiplex PCR followed by template-directed single base extension at each SNP site was conducted with a MassARRAY iPLEX Gold kit (Sequenom) following the manufacturer‘s protocol. The genotypes were determined in MassARRAY Typer 4.0 software (Sequenom).

Watanabe S., Shimizu T., Machita K., Tsubokura Y., Xia Z., Yamada T., Hajika M., Ishimoto M., Katayose Y., Harada K, & Kaga A. (2017). Development of a high-density linkage map and chromosome segment substitution lines for Japanese soybean cultivar Enrei. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 25(2), 123-136.

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SNP Genotyping of Obesity and MS

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We searched the literature and SNP databases to identify candidate SNPs associated with obesity or MS for assessment. A total of 47 SNPs reportedly associated with overweight/obesity, hypertension, and MS in Asian populations were genotyped (16 (link), 17 (link), 24 (link)). Genomic DNA was extracted from peripheral leukocytes using phenol chloroform. The primers and probes for SNP amplification were designed using Sequenom Assay Design 3.1 software (Sequenom, Inc., San Diego, CA, USA). SNP genotyping was conducted using the Mass Array system (Sequenom, Inc.) based on high-throughput multiplex polymerase chain reaction (PCR) amplification of target fragments in a 384-well PCR plate. The PCR products were subjected to uric acidification and primer single-base extension reaction. Alleles were then detected by matrix-assisted laser desorption time-of-flight mass spectrometry (Sequenom, Inc.), and mass spectra analysis was conducted with Mass Array Typer 4.0 software (Sequenom, Inc.).

Ma Z., Wang Y., Xu C., Ai F., Huang L., Wang J., Peng J., Zhou Y., Yin M., Zhang S, & Yang X. (2019). Obesity-Related Genetic Variants and Hyperuricemia Risk in Chinese Men. Frontiers in Endocrinology, 10, 230.

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Genotyping AGTR1 Gene SNPs in Asians

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SNPs within the AGTR1 gene with minor allele frequency (MAF) > 0.05 in the HapMap Asian population were obtained from PubMed databases and single-nucleotide polymorphism (SNP) databases [the dbSNP (NCBI) and the Japanese SNP database (JSNP)]. DNA was extracted from peripheral whole blood cells by the GoldMag-Mini Whole Blood Genomic DNA Purification Kit (GoldMag Co. Ltd. Xian, China) following the manufacturer's protocols, and DNA concentration of each sample was determined by spectrometry (DU530 UV/VIS spectrophotometer, Beckman Instruments, Fullerton, CA, USA). The PCR and extension primers were designed using the MassARRAY Assay Design 3.0 software (Sequenom, Inc.). SNPs were genotyped with the Sequenom MassARRAY RS1000 according to the instructions of the manufacturer [19 ]. We performed data management and analyses using Sequenom MassArray TYPER 4.0 software.

Jin T., Ren Y., Zhu X., Li X., Ouyang Y., He X., Zhang Z., Zhang Y., Kang L, & Yuan D. (2016). Angiotensin II receptor 1 gene variants are associated with high-altitude pulmonary edema risk. Oncotarget, 7(47), 77117-77123.

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MassARRAY Genotyping of de novo Mutations

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A MassARRAY3 Analyzer (Sequenom Inc, San Diego, CA) with iPLEX Gold Genotyping Reagent (Sequenom Inc) was used to validate the 286 candidates, according to the manufacturer's instructions. Briefly, MassARRAY Typer4 Assay Designer (Sequenom Inc) designed the 286 PCR primer pairs and 286 iPLEX primers as single-base extension primers for each candidate. We used 37 genomic DNA samples, including 35 samples from the TOY-KO pedigree and two control samples, as well as C57BL/6J and the original ES cell DNA to determine the origin of the de novo mutations in the TOY-KO pedigree. Ten nanograms of genomic DNA were used in each multiplex PCR for the MassARRAY. After dephosphorylation, single-base extension with the iPLEX primer and desalting were performed. The reaction products were spotted onto a 384-format SpectroCHIP with a MassARRAY Nanodispenser (Sequenom Inc) and then subjected to a MassARRAY 3 analyzer (Sequenom Inc). MassARRAY Typer 4.0 software (Sequenom Inc) was used to analyze the mass spectrum data.

Ohno M., Sakumi K., Fukumura R., Furuichi M., Iwasaki Y., Hokama M., Ikemura T., Tsuzuki T., Gondo Y, & Nakabeppu Y. (2014). 8-oxoguanine causes spontaneous de novo germline mutations in mice. Scientific Reports, 4, 4689.

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